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free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.45 }, "provenance": { "deposit_id": "1XD3", "doi": "10.1074/jbc.M410770200", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1XD3" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of UCHL3-UbVME complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.8, "salt_mM": null, "temperature_c": 29.85 }, "construct": { "description": "PROTEIN (UBIQUITIN CORE MUTANT 1D7) (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1UD7", "evidence_id": "EV-PDB-1UD7-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "1UD7", "doi": "10.1016/S0969-2126(99)80123-3", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1UD7" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "SOLUTION STRUCTURE OF THE DESIGNED HYDROPHOBIC CORE MUTANT OF UBIQUITIN, 1D7" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "UBIQUITIN (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1UBQ", "evidence_id": "EV-PDB-1UBQ-1", "mappings": [ { "confidence": "high", "justification": "Native ubiquitin fold at 1.8 Å; representative for the folded state.", "rule": "curator_assignment", "state_id": "Ub-folded", "who": "curator:draft (unreviewed)" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.8 }, "provenance": { "deposit_id": "1UBQ", "doi": "10.1016/0022-2836(87)90679-6", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1UBQ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "UBIQUITIN (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1UBI", "evidence_id": "EV-PDB-1UBI-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.8 }, "provenance": { "deposit_id": "1UBI", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1UBI" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "SYNTHETIC STRUCTURAL AND BIOLOGICAL STUDIES OF THE UBIQUITIN SYSTEM. PART 1" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "TETRAUBIQUITIN (chains A,B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1TBE", "evidence_id": "EV-PDB-1TBE-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.4 }, "provenance": { "deposit_id": "1TBE", "doi": "10.1006/jmbi.1994.1169", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1TBE" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "STRUCTURE OF TETRAUBIQUITIN SHOWS HOW MULTIUBIQUITIN CHAINS CAN BE FORMED" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.6, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1SIF", "evidence_id": "EV-PDB-1SIF-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.18 }, "provenance": { "deposit_id": "1SIF", "doi": "10.1021/bi0361620", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1SIF" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of a multiple hydrophobic core mutant of ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ACY", "CU", "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 4.6, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "ubiquitin (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1S1Q", "evidence_id": "EV-PDB-1S1Q-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.0 }, "provenance": { "deposit_id": "1S1Q", "doi": "10.1016/S1097-2765(04)00129-7", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1S1Q" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "TSG101(UEV) domain in complex with Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.5, "salt_mM": null, "temperature_c": 17.85 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1Q5W", "evidence_id": "EV-PDB-1Q5W-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "1Q5W", "doi": "10.1038/sj.emboj.7600114", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1Q5W" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Ubiquitin Recognition by Npl4 Zinc-Fingers" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.6, "salt_mM": null, "temperature_c": -163.15 }, "construct": { "description": "UBIQUITIN (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1OGW", "evidence_id": "EV-PDB-1OGW-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.32 }, "provenance": { "deposit_id": "1OGW", "doi": "10.1002/CBIC.200300699", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1OGW" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Synthetic Ubiquitin with fluoro-Leu at 50 and 67" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin aldehyde (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1NBF", "evidence_id": "EV-PDB-1NBF-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.3 }, "provenance": { "deposit_id": "1NBF", "doi": "10.1016/S0092-8674(02)01199-6", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1NBF" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "UBIQUITIN (chains A,B)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1GJZ", "evidence_id": "EV-PDB-1GJZ-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "1GJZ", "doi": "10.1006/JMBI.2001.5181", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1GJZ" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Solution structure of a dimeric N-terminal fragment of human ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": 19.85 }, "construct": { "description": "UBIQUITIN (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1G6J", "evidence_id": "EV-PDB-1G6J-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "1G6J", "doi": "10.1021/ja005766d", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1G6J" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "STRUCTURE OF RECOMBINANT HUMAN UBIQUITIN IN AOT REVERSE MICELLES" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.5, "salt_mM": null, "temperature_c": -243.15 }, "construct": { "description": "UBIQUITIN (chains B)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1FXT", "evidence_id": "EV-PDB-1FXT-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "1FXT", "doi": "10.1016/S0969-2126(01)00657-8", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1FXT" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTER COMPLEX" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 4.5, "salt_mM": null, "temperature_c": -183.15 }, "construct": { "description": "TETRAUBIQUITIN (chains A,B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1F9J", "evidence_id": "EV-PDB-1F9J-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.7 }, "provenance": { "deposit_id": "1F9J", "doi": "10.1107/S090744490001800X", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1F9J" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "STRUCTURE OF A NEW CRYSTAL FORM OF TETRAUBIQUITIN" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": 34.85 }, "construct": { "description": "PROTEIN (UBIQUITIN) (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1D3Z", "evidence_id": "EV-PDB-1D3Z-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "1D3Z", "doi": "10.1021/ja9812610", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1D3Z" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "UBIQUITIN NMR STRUCTURE" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 4.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "PROTEIN (UBIQUITIN YUH1-UBAL) (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1CMX", "evidence_id": "EV-PDB-1CMX-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.25 }, "provenance": { "deposit_id": "1CMX", "doi": "10.1093/emboj/18.14.3877", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1CMX" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL HYDROLASES" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.8, "salt_mM": null, "temperature_c": 29.85 }, "construct": { "description": "PROTEIN (1D8 UBIQUITIN) (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1C3T", "evidence_id": "EV-PDB-1C3T-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "1C3T", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1C3T" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "ROTAMER STRAIN AS A DETERMINANT OF PROTEIN STRUCTURAL SPECIFICITY" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains H,I,J,K)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/11SY", "evidence_id": "EV-PDB-11SY-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 4.28 }, "provenance": { "deposit_id": "11SY", "doi": "10.1101/2025.10.27.684972", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/11SY" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (NPL4 focused)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 4.1, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2L3Z", "evidence_id": "EV-PDB-2L3Z-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2L3Z", "doi": "10.1002/cphc.201100062", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2L3Z" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Proton-Detected 4D DREAM Solid-State NMR Structure of Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2LD9", "evidence_id": "EV-PDB-2LD9-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2LD9", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2LD9" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Backbone Structure of Ubiquitin determined using Backbone amide NOEs and Backbone N-H and N-C RDCs" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.2, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2LVO", "evidence_id": "EV-PDB-2LVO-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2LVO", "doi": "10.1016/j.str.2012.09.020", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2LVO" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Structure of the gp78CUE domain bound to monubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.2, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Ubiquitin (chains A,B)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2LVQ", "evidence_id": "EV-PDB-2LVQ-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2LVQ", "doi": "10.1016/j.str.2012.09.020", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2LVQ" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "gp78CUE domain bound to the proximal ubiquitin of K48-linked diubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.0, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2LZ6", "evidence_id": "EV-PDB-2LZ6-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2LZ6", "doi": "10.1371/journal.pone.0073018", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2LZ6" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Distinct ubiquitin binding modes exhibited by sh3 domains: molecular determinants and functional implications" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.8, "salt_mM": null, "temperature_c": 22.85 }, "construct": { "description": "Ubiquitin (chains A,B)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2MBO", "evidence_id": "EV-PDB-2MBO-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2MBO", "doi": "10.1016/j.str.2013.04.029", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2MBO" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "K11-linked Diubiquitin average solution structure at pH 6.8, 0 mM NaCl" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.2, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2MI8", "evidence_id": "EV-PDB-2MI8-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2MI8", "doi": "10.1002/pro.2450", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2MI8" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Solution structure of lysine-free (K0) ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.6, "salt_mM": null, "temperature_c": 18.85 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2MOR", "evidence_id": "EV-PDB-2MOR-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2MOR", "doi": "10.1021/jp5021824", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2MOR" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "A tensor-free method for the structural and dynamical refinement of proteins using residual dipolar couplings" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Polyubiquitin-C (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2MRE", "evidence_id": "EV-PDB-2MRE-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2MRE", "doi": "10.1021/bi500823h", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2MRE" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "NMR structure of the Rad18-UBZ/ubiquitin complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2NR2", "evidence_id": "EV-PDB-2NR2-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2NR2", "doi": "10.1007/s10858-006-9117-7", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2NR2" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "TB" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2OJR", "evidence_id": "EV-PDB-2OJR-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.6 }, "provenance": { "deposit_id": "2OJR", "doi": "10.1021/ja070481n", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2OJR" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of ubiquitin solved by SAD using the Lanthanide-Binding Tag" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.8, "salt_mM": null, "temperature_c": 36.85 }, "construct": { "description": "ubiquitin (chains A,B)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2RR9", "evidence_id": "EV-PDB-2RR9-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2RR9", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2RR9" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "The solution structure of the K63-Ub2:tUIMs complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.2, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2RU6", "evidence_id": "EV-PDB-2RU6-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2RU6", "doi": "10.1021/bi401617n", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2RU6" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "The pure alternative state of ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CL" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "UBIQUITIN (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2WDT", "evidence_id": "EV-PDB-2WDT-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.3 }, "provenance": { "deposit_id": "2WDT", "doi": "10.1074/JBC.M109.072405", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2WDT" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CL", "EDO", "FLC" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 3.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "UBIQUITIN (chains A,B,C,D,E,F,G,H,I,J,K,L)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2XEW", "evidence_id": "EV-PDB-2XEW-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.2 }, "provenance": { "deposit_id": "2XEW", "doi": "10.1038/NSMB.1873", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2XEW" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of K11-linked diubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2Z59", "evidence_id": "EV-PDB-2Z59-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2Z59", "doi": "10.1038/nature06924", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2Z59" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Complex Structures of Mouse Rpn13 (22-130aa) and ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "UBC protein (chains A,G)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2ZVO", "evidence_id": "EV-PDB-2ZVO-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.9 }, "provenance": { "deposit_id": "2ZVO", "doi": "10.1016/j.cell.2009.03.007", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2ZVO" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "NEMO CoZi domain in complex with diubiquitin in C2 space group" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 4.1, "salt_mM": null, "temperature_c": -178.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3A33", "evidence_id": "EV-PDB-3A33-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.2 }, "provenance": { "deposit_id": "3A33", "doi": "10.1016/j.str.2009.11.007", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3A33" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "UbcH5b~Ubiquitin Conjugate" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A,B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3AUL", "evidence_id": "EV-PDB-3AUL-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.39 }, "provenance": { "deposit_id": "3AUL", "doi": "10.1074/jbc.M111.256354", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3AUL" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of wild-type Lys48-linked diubiquitin in an open conformation" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN", "branched: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A,D,G,J)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3B08", "evidence_id": "EV-PDB-3B08-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.701 }, "provenance": { "deposit_id": "3B08", "doi": "10.1073/pnas.1109088108", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3B08" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "TAM", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3B0A", "evidence_id": "EV-PDB-3B0A-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.9 }, "provenance": { "deposit_id": "3B0A", "doi": "10.1073/pnas.1109088108", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3B0A" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "3CN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3BY4", "evidence_id": "EV-PDB-3BY4-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.55 }, "provenance": { "deposit_id": "3BY4", "doi": "10.1074/jbc.M704398200", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3BY4" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "3CN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3C0R", "evidence_id": "EV-PDB-3C0R-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.315 }, "provenance": { "deposit_id": "3C0R", "doi": "10.1074/jbc.M704398200", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3C0R" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.3, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains V,Y)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3DVN", "evidence_id": "EV-PDB-3DVN-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.7 }, "provenance": { "deposit_id": "3DVN", "doi": "10.1016/j.cell.2008.07.039", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3DVN" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of K63-specific fab Apu2.16 bound to K63-linked di-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.3, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin D77 (chains U,X)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3DVN", "evidence_id": "EV-PDB-3DVN-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.7 }, "provenance": { "deposit_id": "3DVN", "doi": "10.1016/j.cell.2008.07.039", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3DVN" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of K63-specific fab Apu2.16 bound to K63-linked di-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CD" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A,B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3EEC", "evidence_id": "EV-PDB-3EEC-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.0 }, "provenance": { "deposit_id": "3EEC", "doi": "10.1039/b813463d", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3EEC" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "X-ray structure of human ubiquitin Cd(II) adduct" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CD" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.2, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3H7P", "evidence_id": "EV-PDB-3H7P-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.9 }, "provenance": { "deposit_id": "3H7P", "doi": "10.1002/prot.22568", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3H7P" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of K63-linked di-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CD" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.2, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3H7P", "evidence_id": "EV-PDB-3H7P-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.9 }, "provenance": { "deposit_id": "3H7P", "doi": "10.1002/prot.22568", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3H7P" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of K63-linked di-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.2, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A,B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3H7S", "evidence_id": "EV-PDB-3H7S-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.3 }, "provenance": { "deposit_id": "3H7S", "doi": "10.1002/prot.22568", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3H7S" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structures of K63-linked di- and tri-ubiquitin reveal a highly extended chain architecture" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 4.6, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A,B,C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3HM3", "evidence_id": "EV-PDB-3HM3-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.96 }, "provenance": { "deposit_id": "3HM3", "doi": "10.1016/j.jmb.2009.07.090", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3HM3" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "The Structure and conformation of Lys-63 linked tetra-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GVE" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 9.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3IFW", "evidence_id": "EV-PDB-3IFW-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.4 }, "provenance": { "deposit_id": "3IFW", "doi": "10.1073/pnas.0910870107", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3IFW" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of the S18Y variant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester." }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CL", "NEH", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3IHP", "evidence_id": "EV-PDB-3IHP-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.8 }, "provenance": { "deposit_id": "3IHP", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3IHP" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Covalent Ubiquitin-Usp5 Complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.1, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains X,Y)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3JVZ", "evidence_id": "EV-PDB-3JVZ-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.3 }, "provenance": { "deposit_id": "3JVZ", "doi": "10.1016/j.molcel.2009.11.010", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3JVZ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "E2~Ubiquitin-HECT" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.1, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains X,Y)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3JW0", "evidence_id": "EV-PDB-3JW0-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.1 }, "provenance": { "deposit_id": "3JW0", "doi": "10.1016/j.molcel.2009.11.010", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3JW0" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "E2~Ubiquitin-HECT" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3K9O", "evidence_id": "EV-PDB-3K9O-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.8 }, "provenance": { "deposit_id": "3K9O", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3K9O" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "The crystal structure of E2-25K and UBB+1 complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GVE" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 9.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3KVF", "evidence_id": "EV-PDB-3KVF-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.8 }, "provenance": { "deposit_id": "3KVF", "doi": "10.1073/pnas.0910870107", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3KVF" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of the I93M mutant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -183.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3JSV", "evidence_id": "EV-PDB-3JSV-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.7 }, "provenance": { "deposit_id": "3JSV", "doi": "10.1016/j.febslet.2009.09.028", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3JSV" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of mouse NEMO CoZi in complex with Lys63-linked di-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -183.15 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3JSV", "evidence_id": "EV-PDB-3JSV-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.7 }, "provenance": { "deposit_id": "3JSV", "doi": "10.1016/j.febslet.2009.09.028", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3JSV" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of mouse NEMO CoZi in complex with Lys63-linked di-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A,B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3EHV", "evidence_id": "EV-PDB-3EHV-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.81 }, "provenance": { "deposit_id": "3EHV", "doi": "10.1039/b813463d", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3EHV" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "X-ray structure of human ubiquitin Zn(II) adduct" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "HG" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3EFU", "evidence_id": "EV-PDB-3EFU-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.84 }, "provenance": { "deposit_id": "3EFU", "doi": "10.1039/b813463d", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3EFU" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "X-ray structure of human ubiquitin-Hg(II) adduct" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 4.6, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "ubiquitin (chains A,B,C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3ALB", "evidence_id": "EV-PDB-3ALB-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.85 }, "provenance": { "deposit_id": "3ALB", "doi": "10.1016/j.bbrc.2010.08.057", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3ALB" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Cyclic Lys48-linked tetraubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "UBC protein (chains A,C,E,G)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2ZVN", "evidence_id": "EV-PDB-2ZVN-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.0 }, "provenance": { "deposit_id": "2ZVN", "doi": "10.1016/j.cell.2009.03.007", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2ZVN" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "NEMO CoZi domain incomplex with diubiquitin in P212121 space group" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.3, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A,B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2ZCB", "evidence_id": "EV-PDB-2ZCB-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.6 }, "provenance": { "deposit_id": "2ZCB", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2ZCB" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal Structure of ubiquitin P37A/P38A" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CL", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "UBIQUITIN (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2W9N", "evidence_id": "EV-PDB-2W9N-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.25 }, "provenance": { "deposit_id": "2W9N", "doi": "10.1038/EMBOR.2009.55", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2W9N" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "crystal structure of linear di-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.8, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Ubiquitin (chains A,B)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2PEA", "evidence_id": "EV-PDB-2PEA-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2PEA", "doi": "10.1021/ja071185d", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2PEA" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "NMR Based Structure of the Closed Conformation of LYS48-Linked Di-Ubiquitin Using Experimental Global Rotational Diffusion Tensor from NMR Relaxation Measurements" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.8, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Ubiquitin (chains A,B)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2PE9", "evidence_id": "EV-PDB-2PE9-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2PE9", "doi": "10.1021/ja071185d", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2PE9" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "NMR Based Structure of the Open Conformation of LYS48-Linked Di-UBiquitin Using Experimental Global Rotational Diffusion Tensor from NMR Relaxation Measurements" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "MES", "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -150.15 }, "construct": { "description": "Ubiquitin (chains D,H)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2O6V", "evidence_id": "EV-PDB-2O6V-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.2 }, "provenance": { "deposit_id": "2O6V", "doi": "10.1016/j.jmb.2006.12.065", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2O6V" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "MES", "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -150.15 }, "construct": { "description": "Ubiquitin (chains B,F)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2O6V", "evidence_id": "EV-PDB-2O6V-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.2 }, "provenance": { "deposit_id": "2O6V", "doi": "10.1016/j.jmb.2006.12.065", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2O6V" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "MES", "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -150.15 }, "construct": { "description": "Ubiquitin (chains A,C,E,G)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2O6V", "evidence_id": "EV-PDB-2O6V-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.2 }, "provenance": { "deposit_id": "2O6V", "doi": "10.1016/j.jmb.2006.12.065", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2O6V" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "MTN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.0, "salt_mM": null, "temperature_c": 29.85 }, "construct": { "description": "ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2N2K", "evidence_id": "EV-PDB-2N2K-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2N2K", "doi": "10.7554/eLife.05767", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2N2K" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "MTN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.0, "salt_mM": null, "temperature_c": 29.85 }, "construct": { "description": "ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2N2K", "evidence_id": "EV-PDB-2N2K-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2N2K", "doi": "10.7554/eLife.05767", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2N2K" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.8, "salt_mM": null, "temperature_c": 22.85 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2MWS", "evidence_id": "EV-PDB-2MWS-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2MWS", "doi": "10.1016/j.str.2015.01.010", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2MWS" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Structure of the complex of ubiquitin and the ubiquitin-like (UBL) domain of Ddi1" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.6, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Polyubiquitin-C (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2MJ5", "evidence_id": "EV-PDB-2MJ5-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2MJ5", "doi": "10.1074/jbc.M114.555441", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2MJ5" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Structure of the UBA Domain of Human NBR1 in Complex with Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.0, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2MCN", "evidence_id": "EV-PDB-2MCN-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2MCN", "doi": "10.1371/journal.pone.0073018", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2MCN" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.8, "salt_mM": null, "temperature_c": 22.85 }, "construct": { "description": "Ubiquitin (chains A,B)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2MBQ", "evidence_id": "EV-PDB-2MBQ-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2MBQ", "doi": "10.1016/j.str.2013.04.029", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2MBQ" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "K11-linked Diubiquitin average solution structure at pH 6.8, 150 mM NaCl" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.2, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Ubiquitin (chains A,B)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2LVP", "evidence_id": "EV-PDB-2LVP-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "2LVP", "doi": "10.1016/j.str.2012.09.020", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2LVP" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "gp78CUE domain bound to the distal ubiquitin of K48-linked diubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GVE" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 9.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3KW5", "evidence_id": "EV-PDB-3KW5-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.83 }, "provenance": { "deposit_id": "3KW5", "doi": "10.1073/pnas.0910870107", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3KW5" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.0, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains E,F,G)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3LDZ", "evidence_id": "EV-PDB-3LDZ-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.6 }, "provenance": { "deposit_id": "3LDZ", "doi": "10.1038/emboj.2010.6", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3LDZ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of human STAM1 VHS domain in complex with ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "EDO", "GOL", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3MHS", "evidence_id": "EV-PDB-3MHS-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.89 }, "provenance": { "deposit_id": "3MHS", "doi": "10.1126/science.1190049", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3MHS" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CL", "GOL", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.3, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "UBIQUITIN VARIANT UBV.21.4 (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3MTN", "evidence_id": "EV-PDB-3MTN-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.7 }, "provenance": { "deposit_id": "3MTN", "doi": "10.1126/science.1230161", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3MTN" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Usp21 in complex with a ubiquitin-based, USP21-specific inhibitor" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.3, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3N3K", "evidence_id": "EV-PDB-3N3K-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.6 }, "provenance": { "deposit_id": "3N3K", "doi": "10.1126/science.1230161", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3N3K" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "The catalytic domain of USP8 in complex with a USP8 specific inhibitor" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "DIO", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3OFI", "evidence_id": "EV-PDB-3OFI-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.35 }, "provenance": { "deposit_id": "3OFI", "doi": "10.1016/j.jmb.2010.12.026", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3OFI" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of human insulin-degrading enzyme in complex with ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 4.2, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3ONS", "evidence_id": "EV-PDB-3ONS-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.8 }, "provenance": { "deposit_id": "3ONS", "doi": "10.1002/pro.584", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3ONS" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Human Ubiquitin in a new crystal form" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-B (Fragment) (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3PRM", "evidence_id": "EV-PDB-3PRM-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.3 }, "provenance": { "deposit_id": "3PRM", "doi": "10.1128/JVI.02496-10", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3PRM" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "4LJ", "ACT", "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin B (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3PT2", "evidence_id": "EV-PDB-3PT2-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.5 }, "provenance": { "deposit_id": "3PT2", "doi": "10.1073/pnas.1013388108", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3PT2" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of a viral OTU domain protease bound to Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.5, "salt_mM": null, "temperature_c": -180.15 }, "construct": { "description": "Polyubiquitin-B (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3PTF", "evidence_id": "EV-PDB-3PTF-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.7 }, "provenance": { "deposit_id": "3PTF", "doi": "10.1016/j.jmb.2011.03.011", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3PTF" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ribonuclease/Ubiquitin chimeric protein (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3Q3F", "evidence_id": "EV-PDB-3Q3F-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.169 }, "provenance": { "deposit_id": "3Q3F", "doi": "10.1016/j.jmb.2011.12.050", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3Q3F" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Engineering Domain-Swapped Binding Interfaces by Mutually Exclusive Folding: Insertion of Ubiquitin into position 103 of Barnase" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CL", "M12", "MAN", "N1L", "TLA" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -180.15 }, "construct": { "description": "Ubiquitin (chains A,B,C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3RUL", "evidence_id": "EV-PDB-3RUL-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.5 }, "provenance": { "deposit_id": "3RUL", "doi": "10.1021/ja208755j", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3RUL" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "New strategy to analyze structures of glycopeptide-target complexes" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.8, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains B,D,F,H)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3TMP", "evidence_id": "EV-PDB-3TMP-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.91 }, "provenance": { "deposit_id": "3TMP", "doi": "10.1038/nsmb.2206", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3TMP" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "The catalytic domain of human deubiquitinase DUBA in complex with ubiquitin aldehyde" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "linear di-ubiquitin (chains A,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3U30", "evidence_id": "EV-PDB-3U30-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.428 }, "provenance": { "deposit_id": "3U30", "doi": "10.1016/j.jmb.2011.12.053", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3U30" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of a linear-specific Ubiquitin fab bound to linear ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -160.15 }, "construct": { "description": "Polyubiquitin-C (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3UGB", "evidence_id": "EV-PDB-3UGB-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.35 }, "provenance": { "deposit_id": "3UGB", "doi": "10.1021/bi300058m", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3UGB" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "UbcH5c~Ubiquitin Conjugate" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CL", "GOL", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3V6C", "evidence_id": "EV-PDB-3V6C-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.7 }, "provenance": { "deposit_id": "3V6C", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3V6C" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal Structure of USP2 in complex with mutated ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CL", "GOL", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3V6E", "evidence_id": "EV-PDB-3V6E-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.1 }, "provenance": { "deposit_id": "3V6E", "doi": "10.1126/science.1230161", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3V6E" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal Structure of USP2 and a mutant form of Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "K", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A,B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3VUW", "evidence_id": "EV-PDB-3VUW-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.95 }, "provenance": { "deposit_id": "3VUW", "doi": "10.1038/emboj.2012.241", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3VUW" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of A20 ZF7 in complex with linear ubiquitin, form I" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "EDO", "K", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A,B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3VUX", "evidence_id": "EV-PDB-3VUX-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.699 }, "provenance": { "deposit_id": "3VUX", "doi": "10.1038/emboj.2012.241", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3VUX" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of A20 ZF7 in complex with linear ubiquitin, form II" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "K", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A,B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3VUY", "evidence_id": "EV-PDB-3VUY-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.981 }, "provenance": { "deposit_id": "3VUY", "doi": "10.1038/emboj.2012.241", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3VUY" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of A20 ZF7 in complex with linear tetraubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CA", "EDO", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "POLYUBIQUITIN-C (chains D,H,L,P)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3ZNI", "evidence_id": "EV-PDB-3ZNI-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.21 }, "provenance": { "deposit_id": "3ZNI", "doi": "10.1038/NSMB.2621", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3ZNI" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": 13.85 }, "construct": { "description": "POLYUBIQUITIN-C (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3ZNZ", "evidence_id": "EV-PDB-3ZNZ-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.9 }, "provenance": { "deposit_id": "3ZNZ", "doi": "10.1016/J.CELL.2013.05.014", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3ZNZ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of OTULIN OTU domain (C129A) in complex with Met1- di ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.2, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "UBIQUITIN C (chains C,F)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4AP4", "evidence_id": "EV-PDB-4AP4-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.21 }, "provenance": { "deposit_id": "4AP4", "doi": "10.1038/NATURE11376", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4AP4" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Rnf4 - ubch5a - ubiquitin heterotrimeric complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "MG", "NO3" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": 13.85 }, "construct": { "description": "OTUD2 (chains F)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4BOS", "evidence_id": "EV-PDB-4BOS-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.35 }, "provenance": { "deposit_id": "4BOS", "doi": "10.1016/J.CELL.2013.05.046", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4BOS" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "MG", "NO3" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": 13.85 }, "construct": { "description": "POLYUBIQUITIN-C (chains C,E)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4BOS", "evidence_id": "EV-PDB-4BOS-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.35 }, "provenance": { "deposit_id": "4BOS", "doi": "10.1016/J.CELL.2013.05.046", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4BOS" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": 13.85 }, "construct": { "description": "UBIQUITIN-C (chains B,C,E)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4BOZ", "evidence_id": "EV-PDB-4BOZ-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.03 }, "provenance": { "deposit_id": "4BOZ", "doi": "10.1016/J.CELL.2013.05.046", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4BOZ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of OTUD2 OTU domain in complex with K11-linked di ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains D,E,F,G,H,I)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4DDI", "evidence_id": "EV-PDB-4DDI-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.802 }, "provenance": { "deposit_id": "4DDI", "doi": "10.1016/j.molcel.2012.01.011", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4DDI" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of human OTUB1/UbcH5b~Ub/Ub" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains D,H)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4DHJ", "evidence_id": "EV-PDB-4DHJ-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.35 }, "provenance": { "deposit_id": "4DHJ", "doi": "10.1038/nature10911", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4DHJ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin aldehyde (chains B,F,J,M)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4DHJ", "evidence_id": "EV-PDB-4DHJ-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.35 }, "provenance": { "deposit_id": "4DHJ", "doi": "10.1038/nature10911", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4DHJ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains E)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4DHZ", "evidence_id": "EV-PDB-4DHZ-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.11 }, "provenance": { "deposit_id": "4DHZ", "doi": "10.1038/nature10911", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4DHZ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin aldehyde (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4DHZ", "evidence_id": "EV-PDB-4DHZ-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.11 }, "provenance": { "deposit_id": "4DHZ", "doi": "10.1038/nature10911", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4DHZ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL", "NEH" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4FJV", "evidence_id": "EV-PDB-4FJV-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.047 }, "provenance": { "deposit_id": "4FJV", "doi": "10.1371/journal.pone.0115344", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4FJV" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal Structure of Human Otubain2 and Ubiquitin Complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 4.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A,B,C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4HK2", "evidence_id": "EV-PDB-4HK2-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.4 }, "provenance": { "deposit_id": "4HK2", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4HK2" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "U7Ub25.2540" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "4LJ", "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4HXD", "evidence_id": "EV-PDB-4HXD-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.85 }, "provenance": { "deposit_id": "4HXD", "doi": "10.1128/JVI.03252-12", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4HXD" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Diversity of ubiquitin and ISG15 specificity amongst nairoviruses viral ovarian tumor domain proteases" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -180.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4I6L", "evidence_id": "EV-PDB-4I6L-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.488 }, "provenance": { "deposit_id": "4I6L", "doi": "10.1126/science.1230161", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4I6L" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of OTUB1 in complex with ubiquitin variant" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.2, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4IUM", "evidence_id": "EV-PDB-4IUM-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.45 }, "provenance": { "deposit_id": "4IUM", "doi": "10.1073/pnas.1218464110", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4IUM" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "PO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.6, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4JQW", "evidence_id": "EV-PDB-4JQW-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.9 }, "provenance": { "deposit_id": "4JQW", "doi": "10.1371/journal.pone.0104017", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4JQW" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal Structure of a Complex of NOD1 CARD and Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CL", "EDO", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 3.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4K1R", "evidence_id": "EV-PDB-4K1R-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.632 }, "provenance": { "deposit_id": "4K1R", "doi": "10.1021/bi5003162", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4K1R" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain and Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ACT", "EDO", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "ubiquitin (chains A,B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4K7S", "evidence_id": "EV-PDB-4K7S-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.76 }, "provenance": { "deposit_id": "4K7S", "doi": "10.1002/chem.201302229", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4K7S" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Zn2-hUb (human ubiquitin) adduct from a solution 35 mM zinc acetate/1.3 mM hUb" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ACT", "EDO", "PEG", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "ubiquitin (chains A,B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4K7U", "evidence_id": "EV-PDB-4K7U-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.76 }, "provenance": { "deposit_id": "4K7U", "doi": "10.1002/chem.201302229", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4K7U" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Zn2.3-hUb (human ubiquitin) adduct from a solution 70 mM zinc acetate/1.3 mM hUb" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ACT", "EDO", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "ubiquitin (chains A,B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4K7W", "evidence_id": "EV-PDB-4K7W-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.76 }, "provenance": { "deposit_id": "4K7W", "doi": "10.1002/chem.201302229", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4K7W" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 100 mM zinc acetate/1.3 mM hUb" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains C,D,F,H,J,L,N,P,R,T,V,X)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4KSL", "evidence_id": "EV-PDB-4KSL-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.83 }, "provenance": { "deposit_id": "4KSL", "doi": "10.1038/nature12296", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4KSL" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Gumby/Fam105B in complex with linear di-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "EDO", "MG" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.0, "salt_mM": null, "temperature_c": -196.15 }, "construct": { "description": "Ubiquitin (chains D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4LDT", "evidence_id": "EV-PDB-4LDT-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.901 }, "provenance": { "deposit_id": "4LDT", "doi": "10.1038/nsmb.2655", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4LDT" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "EDO", "MG" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.0, "salt_mM": null, "temperature_c": -196.15 }, "construct": { "description": "Ubiquitin aldehyde (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4LDT", "evidence_id": "EV-PDB-4LDT-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.901 }, "provenance": { "deposit_id": "4LDT", "doi": "10.1038/nsmb.2655", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4LDT" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.2, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains E,F)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4LCD", "evidence_id": "EV-PDB-4LCD-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.1 }, "provenance": { "deposit_id": "4LCD", "doi": "10.7554/eLife.00828", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4LCD" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4KSK", "evidence_id": "EV-PDB-4KSK-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.4 }, "provenance": { "deposit_id": "4KSK", "doi": "10.1038/nature12296", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4KSK" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Gumby/Fam105B in complex with ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.5, "salt_mM": null, "temperature_c": -74.9 }, "construct": { "description": "Polyubiquitin-C (chains D,E,F,G,H,I,M,N,O,P,Q,R)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4DDG", "evidence_id": "EV-PDB-4DDG-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.2987 }, "provenance": { "deposit_id": "4DDG", "doi": "10.1016/j.molcel.2012.01.011", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4DDG" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of human OTUB1/UbcH5b~Ub/Ub" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.5, "salt_mM": null, "temperature_c": 13.85 }, "construct": { "description": "UBIQUITIN (chains C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4BVU", "evidence_id": "EV-PDB-4BVU-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.7 }, "provenance": { "deposit_id": "4BVU", "doi": "10.1002/EMBJ.201386386", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4BVU" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of Shigella effector OspG in complex with host UbcH5c- Ubiquitin conjugate" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "POLYUBIQUITIN-C (chains C,F)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4AUQ", "evidence_id": "EV-PDB-4AUQ-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.176 }, "provenance": { "deposit_id": "4AUQ", "doi": "10.1038/NSMB.2379", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4AUQ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of BIRC7-UbcH5b-Ub complex." }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3WXF", "evidence_id": "EV-PDB-3WXF-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.3 }, "provenance": { "deposit_id": "3WXF", "doi": "10.1038/nsmb.2970", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3WXF" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3WXE", "evidence_id": "EV-PDB-3WXE-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.5 }, "provenance": { "deposit_id": "3WXE", "doi": "10.1038/nsmb.2970", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3WXE" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GCS", "MAN", "NAG", "T55" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 4.6, "salt_mM": null, "temperature_c": -180.15 }, "construct": { "description": "ubiquitin, C-terminal fused by Cys-Lys-D-Ala-D-Ala (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3VFK", "evidence_id": "EV-PDB-3VFK-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.8 }, "provenance": { "deposit_id": "3VFK", "doi": "10.1107/S0907444912050469", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3VFK" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "The structure of monodechloro-teicoplanin in complex with its ligand, using ubiquitin as a ligand carrier" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.1, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B,E)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3OJ4", "evidence_id": "EV-PDB-3OJ4-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.4 }, "provenance": { "deposit_id": "3OJ4", "doi": "10.1016/j.molcel.2010.10.009", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3OJ4" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "NA" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains B,D,F,H)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/3O65", "evidence_id": "EV-PDB-3O65-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.7 }, "provenance": { "deposit_id": "3O65", "doi": "10.1074/jbc.M110.177360", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/3O65" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.5, "salt_mM": null, "temperature_c": 3.85 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4MM3", "evidence_id": "EV-PDB-4MM3-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.752 }, "provenance": { "deposit_id": "4MM3", "doi": "10.1371/journal.ppat.1004113", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4MM3" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of SARS-CoV papain-like protease PLpro in complex with ubiquitin aldehyde" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "EDO", "PO4", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4MSM", "evidence_id": "EV-PDB-4MSM-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.74 }, "provenance": { "deposit_id": "4MSM", "doi": "10.1021/bi5003162", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4MSM" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 E286A mutant bound to ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains E,F,G,H,I,J)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4NQK", "evidence_id": "EV-PDB-4NQK-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.7 }, "provenance": { "deposit_id": "4NQK", "doi": "10.1038/nature13140", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4NQK" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of an Ubiquitin complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "UBIQUITIN (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4UN2", "evidence_id": "EV-PDB-4UN2-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.51 }, "provenance": { "deposit_id": "4UN2", "doi": "10.1002/ANIE.201403102", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4UN2" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of the UBA domain of Dsk2 in complex with Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CL", "EDO", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "POLYUBIQUITIN-C (chains B,E)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4V3K", "evidence_id": "EV-PDB-4V3K-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.04 }, "provenance": { "deposit_id": "4V3K", "doi": "10.1016/J.MOLCEL.2015.02.017", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4V3K" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "RNF38-UbcH5B-UB complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "EDO", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "POLYUBIQUITIN-C (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4V3L", "evidence_id": "EV-PDB-4V3L-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.53 }, "provenance": { "deposit_id": "4V3L", "doi": "10.1016/J.MOLCEL.2015.02.017", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4V3L" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "RNF38-UB-UbcH5B-Ub complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A,B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4XOK", "evidence_id": "EV-PDB-4XOK-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.2 }, "provenance": { "deposit_id": "4XOK", "doi": "10.1038/ncomms9361", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4XOK" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Observing the overall rocking motion of a protein in a crystal." }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.33, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A,B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4XOL", "evidence_id": "EV-PDB-4XOL-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.91 }, "provenance": { "deposit_id": "4XOL", "doi": "10.1038/ncomms9361", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4XOL" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Observing the overall rocking motion of a protein in a crystal - Cubic Ubiquitin crystals." }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL", "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.0, "salt_mM": null, "temperature_c": -163.15 }, "construct": { "description": "UBIQUITIN (chains A,B,C,D,E,F,G,H)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5AF4", "evidence_id": "EV-PDB-5AF4-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.85 }, "provenance": { "deposit_id": "5AF4", "doi": "10.1016/J.MOLCEL.2015.01.042", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5AF4" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of Lys33-linked diUb" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.5, "salt_mM": null, "temperature_c": -163.15 }, "construct": { "description": "POLYUBIQUITIN-C (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5AF5", "evidence_id": "EV-PDB-5AF5-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.68 }, "provenance": { "deposit_id": "5AF5", "doi": "10.1016/J.MOLCEL.2015.01.042", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5AF5" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of Lys33-linked triUb S.G. P 212121" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -163.15 }, "construct": { "description": "UBIQUITIN (chains A,B,C,D,E)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5AF6", "evidence_id": "EV-PDB-5AF6-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.4 }, "provenance": { "deposit_id": "5AF6", "doi": "10.1016/J.MOLCEL.2015.01.042", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5AF6" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of Lys33-linked diUb bound to Trabid NZF1" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "EDO", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "POLYUBIQUITIN-C (chains C,F)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5AIU", "evidence_id": "EV-PDB-5AIU-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.21 }, "provenance": { "deposit_id": "5AIU", "doi": "10.1038/NSMB.3052", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5AIU" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "tetra ubiquitin (chains A,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5B83", "evidence_id": "EV-PDB-5B83-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.694 }, "provenance": { "deposit_id": "5B83", "doi": "10.1038/ncomms12547", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5B83" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Optineurin UBAN in complex with linear ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5C7J", "evidence_id": "EV-PDB-5C7J-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.0 }, "provenance": { "deposit_id": "5C7J", "doi": "10.1016/j.molcel.2016.02.005", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5C7J" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5C7M", "evidence_id": "EV-PDB-5C7M-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.03 }, "provenance": { "deposit_id": "5C7M", "doi": "10.1016/j.molcel.2016.02.005", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5C7M" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "CRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -160.15 }, "construct": { "description": "Polyubiquitin-C (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5H07", "evidence_id": "EV-PDB-5H07-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.586 }, "provenance": { "deposit_id": "5H07", "doi": "10.1016/j.str.2016.11.005", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5H07" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "TNIP2-Ub complex, C2 form" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ACT", "EDO", "PEG", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A,B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5NL4", "evidence_id": "EV-PDB-5NL4-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.32 }, "provenance": { "deposit_id": "5NL4", "doi": "10.1002/chem.201705543", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5NL4" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/1.3 mM E16V hUb" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ACT", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A,B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5NLF", "evidence_id": "EV-PDB-5NLF-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.5 }, "provenance": { "deposit_id": "5NLF", "doi": "10.1002/chem.201705543", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5NLF" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100 mM zinc acetate/1.3 mM E16V hUb" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ACT", "EDO", "ETF", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A,B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5NLI", "evidence_id": "EV-PDB-5NLI-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.53 }, "provenance": { "deposit_id": "5NLI", "doi": "10.1002/chem.201705543", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5NLI" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Zn2-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/10% v/v TFE/1.3 mM E16V hUb" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": 13.85 }, "construct": { "description": "Polyubiquitin-C (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5OE7", "evidence_id": "EV-PDB-5OE7-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.95 }, "provenance": { "deposit_id": "5OE7", "doi": "10.1016/j.chembiol.2017.08.006", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5OE7" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of OTULIN bound to the Met1-linked diubiquitin activity probe" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL", "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.2, "salt_mM": null, "temperature_c": -163.15 }, "construct": { "description": "Ubiquitin (chains A,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5OHV", "evidence_id": "EV-PDB-5OHV-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.801 }, "provenance": { "deposit_id": "5OHV", "doi": "10.1016/j.molcel.2017.08.020", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5OHV" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "K33-specific affimer bound to K33 diUb" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 9.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin T66V/L67N mutant (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5OXH", "evidence_id": "EV-PDB-5OXH-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.601 }, "provenance": { "deposit_id": "5OXH", "doi": "10.15252/embj.201797876", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5OXH" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "C-terminally retracted ubiquitin T66V/L67N mutant" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin L67S mutant (chains A,B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5OXI", "evidence_id": "EV-PDB-5OXI-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.63 }, "provenance": { "deposit_id": "5OXI", "doi": "10.15252/embj.201797876", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5OXI" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "C-terminally retracted ubiquitin L67S mutant" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin C variant (chains E)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5UDH", "evidence_id": "EV-PDB-5UDH-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.24 }, "provenance": { "deposit_id": "5UDH", "doi": "10.1016/j.str.2017.04.013", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5UDH" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "HHARI/ARIH1-UBCH7~Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.5, "salt_mM": null, "temperature_c": 25.0 }, "construct": { "description": "ubiquitin (chains A,B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5WQ4", "evidence_id": "EV-PDB-5WQ4-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.0 }, "provenance": { "deposit_id": "5WQ4", "doi": "10.1080/15548627.2017.1391970", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5WQ4" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of OPTN and linear diubiquitin complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -80.15 }, "construct": { "description": "Ubiquitin (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5ZQ3", "evidence_id": "EV-PDB-5ZQ3-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.182 }, "provenance": { "deposit_id": "5ZQ3", "doi": "10.1016/j.cell.2018.04.023", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5ZQ3" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "PDE-Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AMP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -80.15 }, "construct": { "description": "ubiquitin (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5ZQ4", "evidence_id": "EV-PDB-5ZQ4-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.217 }, "provenance": { "deposit_id": "5ZQ4", "doi": "10.1016/j.cell.2018.04.023", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5ZQ4" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "PDE-Ubi-ADPr" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -80.15 }, "construct": { "description": "Ubiquitin (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5ZQ5", "evidence_id": "EV-PDB-5ZQ5-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.487 }, "provenance": { "deposit_id": "5ZQ5", "doi": "10.1016/j.cell.2018.04.023", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5ZQ5" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "SidE-Ubi" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ADP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -80.15 }, "construct": { "description": "Ubiquitin (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5ZQ6", "evidence_id": "EV-PDB-5ZQ6-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.009 }, "provenance": { "deposit_id": "5ZQ6", "doi": "10.1016/j.cell.2018.04.023", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5ZQ6" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "SidE-Ubi-ADPr" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AMP", "NAD" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -80.15 }, "construct": { "description": "Ubiquitin (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5ZQ7", "evidence_id": "EV-PDB-5ZQ7-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.847 }, "provenance": { "deposit_id": "5ZQ7", "doi": "10.1016/j.cell.2018.04.023", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5ZQ7" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "SidE-Ubi-NAD" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ACY" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.5, "salt_mM": null, "temperature_c": -183.15 }, "construct": { "description": "RNA-directed DNA polymerase homolog (R1),Polyubiquitin-C (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6A43", "evidence_id": "EV-PDB-6A43-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.4 }, "provenance": { "deposit_id": "6A43", "doi": "10.1021/jacs.8b07512", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6A43" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "R1EN(5-225)-ubiquitin fusion" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ACY" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.3, "salt_mM": null, "temperature_c": -183.15 }, "construct": { "description": "RNA-directed DNA polymerase homolog (R1),Polyubiquitin-C (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6A44", "evidence_id": "EV-PDB-6A44-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.4 }, "provenance": { "deposit_id": "6A44", "doi": "10.1021/jacs.8b07512", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6A44" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "R1EN(5-227)-ubiquitin fusion" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6AQR", "evidence_id": "EV-PDB-6AQR-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.1 }, "provenance": { "deposit_id": "6AQR", "doi": "10.15252/embr.201745680", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6AQR" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6B7M", "evidence_id": "EV-PDB-6B7M-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.7 }, "provenance": { "deposit_id": "6B7M", "doi": "10.1038/s41586-018-0147-6", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6B7M" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Legionella effector sdeD (lpg2509) in complex with Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AR6" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6B7O", "evidence_id": "EV-PDB-6B7O-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.85 }, "provenance": { "deposit_id": "6B7O", "doi": "10.1038/s41586-018-0147-6", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6B7O" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Legionella effector sdeD (lpg2509) H67A in complex with ADP-ribosylated Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6EQI", "evidence_id": "EV-PDB-6EQI-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.1 }, "provenance": { "deposit_id": "6EQI", "doi": "10.1038/nature24645", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6EQI" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of PINK1 bound to ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "APR", "MG", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6K2U", "evidence_id": "EV-PDB-6K2U-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.554 }, "provenance": { "deposit_id": "6K2U", "doi": "10.1016/j.molcel.2020.03.016", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6K2U" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Thr66 ADP-ribosylated ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "phosphoubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6N13", "evidence_id": "EV-PDB-6N13-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "6N13", "doi": "10.15252/embj.2018100014", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6N13" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6N6R", "evidence_id": "EV-PDB-6N6R-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.95 }, "provenance": { "deposit_id": "6N6R", "doi": "10.1016/j.jmb.2019.06.012", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6N6R" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of ABIN-1 UBAN in complex with two M1-linked di-ubiquitins" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SAM" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains L)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6NQA", "evidence_id": "EV-PDB-6NQA-7", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.54 }, "provenance": { "deposit_id": "6NQA", "doi": "10.1016/j.cell.2019.02.002", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6NQA" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A,B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6NXK", "evidence_id": "EV-PDB-6NXK-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.2 }, "provenance": { "deposit_id": "6NXK", "doi": "10.1073/pnas.1902889116", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6NXK" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Ubiquitin binding variants" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "EDO" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 4.8, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "ubiquitin (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6OI4", "evidence_id": "EV-PDB-6OI4-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.76 }, "provenance": { "deposit_id": "6OI4", "doi": "10.1074/jbc.AC119.008881", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6OI4" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "RPN13 (19-132)-RPN2 (940-952) pY950-Ub complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 9.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains E)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6P5B", "evidence_id": "EV-PDB-6P5B-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.099 }, "provenance": { "deposit_id": "6P5B", "doi": "10.1038/s41467-020-16211-x", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6P5B" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal Structure of MavC in Complex with Ub-UbE2N" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "K" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6Q00", "evidence_id": "EV-PDB-6Q00-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 0.85 }, "provenance": { "deposit_id": "6Q00", "doi": "10.1093/nar/gkaa318", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6Q00" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains G)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6KBE", "evidence_id": "EV-PDB-6KBE-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.339 }, "provenance": { "deposit_id": "6KBE", "doi": "10.1038/s41467-022-32364-3", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6KBE" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of Deubiquitinase" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ACT", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A,B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5NMC", "evidence_id": "EV-PDB-5NMC-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.7 }, "provenance": { "deposit_id": "5NMC", "doi": "10.1002/chem.201705543", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5NMC" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM hUb" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ACT", "NI" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "ubiquitin (chains B,E)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/5E6J", "evidence_id": "EV-PDB-5E6J-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.85 }, "provenance": { "deposit_id": "5E6J", "doi": "10.1016/j.molcel.2016.04.016", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/5E6J" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "ubiquitin (chains A,B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4ZQS", "evidence_id": "EV-PDB-4ZQS-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.804 }, "provenance": { "deposit_id": "4ZQS", "doi": "10.1107/S2059798316001510", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4ZQS" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "New compact conformation of linear Ub2 structure" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "EDO", "PO4", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.3, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4MSQ", "evidence_id": "EV-PDB-4MSQ-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.952 }, "provenance": { "deposit_id": "4MSQ", "doi": "10.1021/bi5003162", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4MSQ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 catalytic domain bound to ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "U94" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains E,F,G,H)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/4MDK", "evidence_id": "EV-PDB-4MDK-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.6095 }, "provenance": { "deposit_id": "4MDK", "doi": "10.1038/nchembio.1412", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/4MDK" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Cdc34-ubiquitin-CC0651 complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "BR", "CL", "EDO", "K" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.5, "salt_mM": null, "temperature_c": -193.15 }, "construct": { "description": "Polyubiquitin-C (chains C,F)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6QML", "evidence_id": "EV-PDB-6QML-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.1 }, "provenance": { "deposit_id": "6QML", "doi": "10.1016/j.chembiol.2020.11.005", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6QML" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "UCHL3 in complex with synthetic, K27-linked diubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains B,D,F)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6RYA", "evidence_id": "EV-PDB-6RYA-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.21 }, "provenance": { "deposit_id": "6RYA", "doi": "10.1016/j.molcel.2019.10.019", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6RYA" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of Dup1 mutant H67A:Ubiquitin complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "MPD", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains D,F,J,L)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6S53", "evidence_id": "EV-PDB-6S53-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.8 }, "provenance": { "deposit_id": "6S53", "doi": "10.1038/s41467-019-12388-y", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6S53" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "EDO", "NO3", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains I)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6SQR", "evidence_id": "EV-PDB-6SQR-6", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.18 }, "provenance": { "deposit_id": "6SQR", "doi": "10.1038/s41467-020-15783-y", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6SQR" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "LWZ", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6T7F", "evidence_id": "EV-PDB-6T7F-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.58 }, "provenance": { "deposit_id": "6T7F", "doi": "10.1038/s41589-020-0598-6", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6T7F" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "RCR E3 ligase E2-Ubiquitin transthiolation intermediate" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains U)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6TTU", "evidence_id": "EV-PDB-6TTU-7", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.7 }, "provenance": { "deposit_id": "6TTU", "doi": "10.1038/s41586-020-2000-y", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6TTU" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 8.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains D,H,L)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6TUV", "evidence_id": "EV-PDB-6TUV-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.16 }, "provenance": { "deposit_id": "6TUV", "doi": "10.1016/j.molcel.2021.08.024", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6TUV" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Mindy1 in complex with Lys48 linked di-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CL", "NA" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains D,H,L)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6TXB", "evidence_id": "EV-PDB-6TXB-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.18 }, "provenance": { "deposit_id": "6TXB", "doi": "10.1016/j.molcel.2021.08.024", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6TXB" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Mindy1 mutant (P138A) in complex with Lys48 linked di-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains E)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6UMP", "evidence_id": "EV-PDB-6UMP-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.8 }, "provenance": { "deposit_id": "6UMP", "doi": "10.1038/s41467-020-16211-x", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6UMP" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of MavC in complex with substrate mimic in P65 space group" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.5, "salt_mM": null, "temperature_c": 34.85 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6V5D", "evidence_id": "EV-PDB-6V5D-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "6V5D", "doi": "10.1007/s10858-019-00288-8", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6V5D" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "EROS3 RDC and NOE Derived Ubiquitin Ensemble" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains C,D)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6VAE", "evidence_id": "EV-PDB-6VAE-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.6 }, "provenance": { "deposit_id": "6VAE", "doi": "10.1038/s41586-020-2110-6", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6VAE" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Mono-ubiquitinated Fanconi Anemia ID complex bound to ICL DNA" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains D)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6VAF", "evidence_id": "EV-PDB-6VAF-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.9 }, "provenance": { "deposit_id": "6VAF", "doi": "10.1038/s41586-020-2110-6", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6VAF" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Structure of mono-ubiquitinated FANCD2 bound to non-ubiquitinated FANCI and to DNA" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SAM", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains K)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6VEN", "evidence_id": "EV-PDB-6VEN-7", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.37 }, "provenance": { "deposit_id": "6VEN", "doi": "10.7554/eLife.53199", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6VEN" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Yeast COMPASS in complex with a ubiquitinated nucleosome" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "IOD", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains C,F,I)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6W9D", "evidence_id": "EV-PDB-6W9D-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.19 }, "provenance": { "deposit_id": "6W9D", "doi": "10.1016/j.jmb.2020.05.001", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6W9D" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "RNF12 RING domain in complex with a Ube2d2~Ub conjugate" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ADP", "AGS", "MG", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains u)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6WJD", "evidence_id": "EV-PDB-6WJD-19", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 4.8 }, "provenance": { "deposit_id": "6WJD", "doi": "10.1016/j.str.2020.07.011", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6WJD" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "SA-like state of human 26S Proteasome with non-cleavable M1-linked hexaubiquitin and E3 ubiquitin ligase E6AP/UBE3A" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "MG", "SAH", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains F,T)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6WKR", "evidence_id": "EV-PDB-6WKR-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.5 }, "provenance": { "deposit_id": "6WKR", "doi": "10.1126/science.abc3393", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6WKR" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 9.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6WTG", "evidence_id": "EV-PDB-6WTG-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.63 }, "provenance": { "deposit_id": "6WTG", "doi": "10.1021/acs.biochem.0c00760", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6WTG" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "SdeA DUB Domain in complex with Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GVE" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6YPT", "evidence_id": "EV-PDB-6YPT-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.663 }, "provenance": { "deposit_id": "6YPT", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6YPT" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "X-ray structure of Turnip Yellow Mosaic Virus PRO/DUB in complex with Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "K", "PG4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains C,D,E,F,G,H,I)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6Z7V", "evidence_id": "EV-PDB-6Z7V-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.65 }, "provenance": { "deposit_id": "6Z7V", "doi": "10.1016/j.molcel.2021.08.024", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6Z7V" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Mindy2 (C266A) in complex with Lys48 linked di-ubiquitin (K48-Ub2)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SY8", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains U)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7B5L", "evidence_id": "EV-PDB-7B5L-6", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.8 }, "provenance": { "deposit_id": "7B5L", "doi": "10.1038/s41586-021-03197-9", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/7B5L" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains U)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7B5M", "evidence_id": "EV-PDB-7B5M-6", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.91 }, "provenance": { "deposit_id": "7B5M", "doi": "10.1038/s41586-021-03197-9", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/7B5M" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SY8", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains U)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7B5N", "evidence_id": "EV-PDB-7B5N-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.6 }, "provenance": { "deposit_id": "7B5N", "doi": "10.1038/s41586-021-03197-9", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/7B5N" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1." }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7BBD", "evidence_id": "EV-PDB-7BBD-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.2 }, "provenance": { "deposit_id": "7BBD", "doi": "10.1038/s41467-021-21443-6", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/7BBD" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains C,F,I)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7BBF", "evidence_id": "EV-PDB-7BBF-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.54 }, "provenance": { "deposit_id": "7BBF", "doi": "10.1038/s41467-021-21443-6", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/7BBF" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of ubiquitin charged Ube2N (Ube2N~Ub) in complex with Ube2V2" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -193.15 }, "construct": { "description": "Polyubiquitin-C (chains D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7BXG", "evidence_id": "EV-PDB-7BXG-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.705 }, "provenance": { "deposit_id": "7BXG", "doi": "10.1038/s41467-020-16587-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/7BXG" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "MavC-UBE2N-Ub complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -160.15 }, "construct": { "description": "Polyubiquitin-C (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7EAO", "evidence_id": "EV-PDB-7EAO-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.9 }, "provenance": { "deposit_id": "7EAO", "doi": "10.1016/j.jmb.2021.167116", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/7EAO" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "The structure of the A20-binding inhibitor of NF-kB 1 in complex with tri-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.0, "salt_mM": null, "temperature_c": -160.15 }, "construct": { "description": "tetra ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7EB9", "evidence_id": "EV-PDB-7EB9-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.2 }, "provenance": { "deposit_id": "7EB9", "doi": "10.1016/j.jmb.2021.167116", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/7EB9" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "The structure of the A20-binding inhibitor of NF-kB 1 in complex with tetra-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SAM" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains L)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7K6P", "evidence_id": "EV-PDB-7K6P-8", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.2 }, "provenance": { "deposit_id": "7K6P", "doi": "10.1126/science.abc6663", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/7K6P" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Active state Dot1 bound to the unacetylated H4 nucleosome" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "PO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.4, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains C,D,G,H)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7KEO", "evidence_id": "EV-PDB-7KEO-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.9 }, "provenance": { "deposit_id": "7KEO", "doi": "10.1038/s41589-021-00823-5", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/7KEO" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of K29-linked di-ubiquitin in complex with synthetic antigen binding fragment" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7M4M", "evidence_id": "EV-PDB-7M4M-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.39 }, "provenance": { "deposit_id": "7M4M", "doi": "10.1016/j.molcel.2021.12.005", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/7M4M" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of RBR E3 ligase RNF216 with ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL", "SO4", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.9, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains C,D,E,F)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7M4N", "evidence_id": "EV-PDB-7M4N-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.52 }, "provenance": { "deposit_id": "7M4N", "doi": "10.1016/j.molcel.2021.12.005", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/7M4N" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7MEX", "evidence_id": "EV-PDB-7MEX-1", "mappings": [ { "confidence": "medium", "justification": "Experimental 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"conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 4.2, "salt_mM": null, "temperature_c": -63.15 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7OWD", "evidence_id": "EV-PDB-7OWD-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.71 }, "provenance": { "deposit_id": "7OWD", "doi": 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"source_kind": "deposit", "technique": "xray", "title": "Ubiquitin variant UbV.k.1 in complex with Ube2k" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL", "PG0", "SO4", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.22, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7M4O", "evidence_id": "EV-PDB-7M4O-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", 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and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains E)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6UMS", "evidence_id": "EV-PDB-6UMS-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.344 }, "provenance": { "deposit_id": "6UMS", "doi": "10.1038/s41467-020-16211-x", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6UMS" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of MavC in complex with its substrate mimic in C222(1) space group" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 4.6, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains E)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6ULH", "evidence_id": "EV-PDB-6ULH-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.968 }, "provenance": { "deposit_id": "6ULH", "doi": "10.1038/s41467-020-16211-x", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6ULH" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of MavC in complex with its substrate in R3 spacegroup" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6TNF", "evidence_id": "EV-PDB-6TNF-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.8 }, "provenance": { "deposit_id": "6TNF", "doi": "10.1038/s41594-020-0380-1", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6TNF" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Structure of monoubiquitinated FANCD2 in complex with FANCI and DNA" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains O)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/6T9L", "evidence_id": "EV-PDB-6T9L-12", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.6 }, "provenance": { "deposit_id": "6T9L", "doi": "10.1038/s41586-020-1933-5", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/6T9L" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "SAGA DUB module bound to a ubiqitinated nucleosome" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7YUI", "evidence_id": "EV-PDB-7YUI-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.599 }, "provenance": { "deposit_id": "7YUI", "doi": "10.1126/sciadv.adi4599", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/7YUI" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of HOIL-1L(195-423) in complex with the linear tetra-ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains C,F,I,L)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/7ZJ3", "evidence_id": "EV-PDB-7ZJ3-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.53 }, "provenance": { "deposit_id": "7ZJ3", "doi": "10.1038/s41467-022-35300-7", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/7ZJ3" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8A9J", "evidence_id": "EV-PDB-8A9J-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.8 }, "provenance": { "deposit_id": "8A9J", "doi": "10.1126/sciadv.abq6353", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8A9J" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 without ML323 (consensus reconstruction)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "JDA", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8A9K", "evidence_id": "EV-PDB-8A9K-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.85 }, "provenance": { "deposit_id": "8A9K", "doi": "10.1126/sciadv.abq6353", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8A9K" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with ML323 (consensus reconstruction)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AYE", "CIT" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8ADB", "evidence_id": "EV-PDB-8ADB-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.73 }, "provenance": { "deposit_id": "8ADB", "doi": "10.1038/s41467-022-35244-y", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8ADB" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Viral tegument-like DUBs" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains U)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8B3G", "evidence_id": "EV-PDB-8B3G-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 4.4 }, "provenance": { "deposit_id": "8B3G", "doi": "10.1038/s41594-023-01207-0", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8B3G" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "C(N)RL4CSA-UVSSA-E2-ubiquitin complex." }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8E7O", "evidence_id": "EV-PDB-8E7O-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.7 }, "provenance": { "deposit_id": "8E7O", "doi": "10.1038/s41467-023-43025-4", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8E7O" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "CRYSTAL STRUCTURE OF LYS48-LINKED TETRAUBIQUITIN" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A,B,C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8E7O", "evidence_id": "EV-PDB-8E7O-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.7 }, "provenance": { "deposit_id": "8E7O", "doi": "10.1038/s41467-023-43025-4", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8E7O" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "CRYSTAL STRUCTURE OF LYS48-LINKED TETRAUBIQUITIN" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.2, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains E,F,G,H)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8EAZ", "evidence_id": "EV-PDB-8EAZ-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.08 }, "provenance": { "deposit_id": "8EAZ", "doi": "10.1038/s41467-023-35871-z", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8EAZ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "HOIL-1/E2-Ub/Ub transthiolation complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SO4", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.9, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8EB0", "evidence_id": "EV-PDB-8EB0-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.03 }, "provenance": { "deposit_id": "8EB0", "doi": "10.1038/s41467-023-35871-z", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8EB0" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "RNF216/E2-Ub/Ub transthiolation complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZTO" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 4.6, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8FTQ", "evidence_id": "EV-PDB-8FTQ-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": 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"data_level": "processed", "data_link": "https://www.rcsb.org/structure/8JRT", "evidence_id": "EV-PDB-8JRT-26", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.6 }, "provenance": { "deposit_id": "8JRT", "doi": "10.1038/s41467-025-64719-x", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8JRT" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) bound to K11/K48-branched ubiquitin (Ub) chain composed of three Ub." }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ADP", "ATP", "MG" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-B (chains u,v,w,x)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8JTI", "evidence_id": "EV-PDB-8JTI-26", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.8 }, "provenance": { "deposit_id": "8JTI", "doi": "10.1038/s41467-025-64719-x", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8JTI" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub." }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ANP", "AR6" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-B (chains C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8K6E", "evidence_id": "EV-PDB-8K6E-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.74 }, "provenance": { "deposit_id": "8K6E", "doi": "10.1038/s41589-025-01945-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8K6E" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "LnaB-Actin-PRUb ternary complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AR6", "ATP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains E,F)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8K6F", "evidence_id": "EV-PDB-8K6F-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.41 }, "provenance": { "deposit_id": "8K6F", "doi": "10.1038/s41589-025-01945-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8K6F" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "LnaB-Actin-PRUb ternary complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AR6", "PO4" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "ubiquitin (chains E,F)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8K6I", "evidence_id": "EV-PDB-8K6I-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.19 }, "provenance": { "deposit_id": "8K6I", "doi": "10.1038/s41589-025-01945-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8K6I" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "LnaB-Actin-PRUb ternary complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ANP", "AR6" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8K6R", "evidence_id": "EV-PDB-8K6R-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.76 }, "provenance": { "deposit_id": "8K6R", "doi": "10.1038/s41589-025-01945-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8K6R" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "LnaB-Actin-PRUb ternary complex in the presence of AMPPNP" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ANP", "AR6" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8K6V", "evidence_id": "EV-PDB-8K6V-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.6 }, "provenance": { "deposit_id": "8K6V", "doi": "10.1038/s41589-025-01945-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8K6V" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "LnaB-Actin-PRUb ternary complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains Fa)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8OFF", "evidence_id": "EV-PDB-8OFF-7", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.4 }, "provenance": { "deposit_id": "8OFF", "doi": "10.1093/nar/gkad793", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8OFF" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains u)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8PJN", "evidence_id": "EV-PDB-8PJN-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.4 }, "provenance": { "deposit_id": "8PJN", "doi": "10.1016/j.molcel.2023.11.027", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8PJN" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Catalytic module of human CTLH E3 ligase bound to multiphosphorylated UBE2H~ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains U)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8PMQ", "evidence_id": "EV-PDB-8PMQ-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.53 }, "provenance": { "deposit_id": "8PMQ", "doi": "10.1016/j.molcel.2023.11.027", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8PMQ" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Catalytic module of yeast GID E3 ligase bound to multiphosphorylated Ubc8~ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SY8", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains U)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8PQL", "evidence_id": "EV-PDB-8PQL-5", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.76 }, "provenance": { "deposit_id": "8PQL", "doi": "10.1038/s41594-023-01206-1", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8PQL" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SY8", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C,Nucleotide exchange factor SIL1 (chains E)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8PQL", "evidence_id": "EV-PDB-8PQL-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.76 }, "provenance": { "deposit_id": "8PQL", "doi": "10.1038/s41594-023-01206-1", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8PQL" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin carboxyl-terminal hydrolase MINDY (chains A,B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8Q06", "evidence_id": "EV-PDB-8Q06-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.9 }, "provenance": { "deposit_id": "8Q06", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8Q06" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "EF-hand of MINDY3 Deubiquitylase in Complex with UBL of RAD23A" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "U9O", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains U)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8Q7R", "evidence_id": "EV-PDB-8Q7R-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.71 }, "provenance": { "deposit_id": "8Q7R", "doi": "10.1016/j.molcel.2024.01.022", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8Q7R" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "759", "SY8", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains U)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8R5H", "evidence_id": "EV-PDB-8R5H-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.44 }, "provenance": { "deposit_id": "8R5H", "doi": "10.1016/j.molcel.2024.01.022", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8R5H" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "759", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-B (chains U)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8RX0", "evidence_id": "EV-PDB-8RX0-9", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.7 }, "provenance": { "deposit_id": "8RX0", "doi": "10.1126/sciadv.ado6492", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8RX0" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "(NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AYE", "GOL" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8SSI", "evidence_id": "EV-PDB-8SSI-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.5 }, "provenance": { "deposit_id": "8SSI", "doi": "10.1016/j.chom.2024.04.012", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8SSI" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of Burkholderia pseudomallei deubiquitinase TssM in complex with ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AYE" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8ST8", "evidence_id": "EV-PDB-8ST8-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.75 }, "provenance": { "deposit_id": "8ST8", "doi": "10.1016/j.molcel.2023.11.017", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8ST8" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of E3 ligase SopA bound to ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AYE" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8ST9", "evidence_id": "EV-PDB-8ST9-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.5 }, "provenance": { "deposit_id": "8ST9", "doi": "10.1016/j.molcel.2023.11.017", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8ST9" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of E3 ligase NleL bound to ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains M)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8SVF", "evidence_id": "EV-PDB-8SVF-9", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.2 }, "provenance": { "deposit_id": "8SVF", "doi": "10.1126/sciadv.adg9832", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8SVF" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BAP1/ASXL1 bound to the H2AK119Ub Nucleosome" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL", "LI" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Di-Ubiquitin (chains A,B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8T48", "evidence_id": "EV-PDB-8T48-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.0 }, "provenance": { "deposit_id": "8T48", "doi": "10.1016/j.immuni.2024.04.004", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8T48" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "The N4BP1 CUE-like domain in complex with linear di-Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains D)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8U5H", "evidence_id": "EV-PDB-8U5H-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.23 }, "provenance": { "deposit_id": "8U5H", "doi": "10.1038/s41467-024-50526-3", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8U5H" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains i,j)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8ZDC", "evidence_id": "EV-PDB-8ZDC-37", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.8 }, "provenance": { "deposit_id": "8ZDC", "doi": "10.1016/j.molcel.2025.01.013", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8ZDC" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of the human ubiquitylated pre-40S ribosome with RIOK3" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains i,j)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8ZDD", "evidence_id": "EV-PDB-8ZDD-36", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.7 }, "provenance": { "deposit_id": "8ZDD", "doi": "10.1016/j.molcel.2025.01.013", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8ZDD" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of the human ubiquitylated pre-40S ribosome with RIOK3 (without NOB1)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains A,B)", "labels": [] }, "data_format": "mmCIF/IHM", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8ZZ4", "evidence_id": "EV-PDB-8ZZ4-1", "mappings": [], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "8ZZ4", "doi": "10.1021/acs.biochem.7b00817", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8ZZ4" }, "reader": null, "source_kind": "deposit", "technique": "integrative", "title": "Structure of K63-linked Diubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF/IHM", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9A1L", "evidence_id": "EV-PDB-9A1L-2", "mappings": [], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "9A1L", "doi": "10.1038/s41420-024-01913-8", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9A1L" }, "reader": null, "source_kind": "deposit", "technique": "integrative", "title": "N4BP1 CUE domain in complex with ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9D1I", "evidence_id": "EV-PDB-9D1I-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.0 }, "provenance": { "deposit_id": "9D1I", "doi": "10.1038/s41467-024-54126-z", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9D1I" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of Ubiquitin bound to KLHDC3-EloB/C" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9D1Y", "evidence_id": "EV-PDB-9D1Y-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.6 }, "provenance": { "deposit_id": "9D1Y", "doi": "10.1038/s41467-024-54126-z", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9D1Y" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of G75R Ubiquitin bound to KLHDC3-EloB/C" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "MPD" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9D1Z", "evidence_id": "EV-PDB-9D1Z-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.88 }, "provenance": { "deposit_id": "9D1Z", "doi": "10.1038/s41467-024-54126-z", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9D1Z" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of G75Q Ubiquitin bound to KLHDC3-EloB/C" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin-C (chains D)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9D8P", "evidence_id": "EV-PDB-9D8P-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.2 }, "provenance": { "deposit_id": "9D8P", "doi": "10.1038/s41467-024-54126-z", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9D8P" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Focused map of Cryo-EM structure of Ubiquitin C-degron bound to KLHDC10-EloB/C" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains N)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9DBY", "evidence_id": "EV-PDB-9DBY-11", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.8 }, "provenance": { "deposit_id": "9DBY", "doi": "10.1038/s41586-024-08183-5", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9DBY" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains N)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9DDE", "evidence_id": "EV-PDB-9DDE-10", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.2 }, "provenance": { "deposit_id": "9DDE", "doi": "10.1038/s41586-024-08183-5", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9DDE" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains N)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9DG3", "evidence_id": "EV-PDB-9DG3-9", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.46 }, "provenance": { "deposit_id": "9DG3", "doi": "10.1038/s41586-024-08183-5", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9DG3" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "A1A4Y", "A1IB8", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9DI1", "evidence_id": "EV-PDB-9DI1-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.7 }, "provenance": { "deposit_id": "9DI1", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9DI1" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of the USP1-UAF1-Ubiquitin complex inhibited by KSQ-4279" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "A1A4Y", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9DI2", "evidence_id": "EV-PDB-9DI2-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.6 }, "provenance": { "deposit_id": "9DI2", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9DI2" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of the USP1-UAF1-Ubiquitin-VS complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains U,V,W,X)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9DNS", "evidence_id": "EV-PDB-9DNS-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.8 }, "provenance": { "deposit_id": "9DNS", "doi": "10.1016/j.celrep.2025.115688", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9DNS" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of Tom1-UBE2D2-ubiquitin complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CL", "SO4", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.2, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9EGV", "evidence_id": "EV-PDB-9EGV-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.0 }, "provenance": { "deposit_id": "9EGV", "doi": "10.26508/lsa.202503243", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9EGV" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "HOIL-1 RING2 domain bound to ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CL", "SO4", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains C)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9EGW", "evidence_id": "EV-PDB-9EGW-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.78 }, "provenance": { "deposit_id": "9EGW", "doi": "10.26508/lsa.202503243", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9EGW" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "HOIL-1 RING2 domain bound to ubiquitin-maltose (maltose not modelled)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "A1A4Y", "A1BHF", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9EBS", "evidence_id": "EV-PDB-9EBS-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.3 }, "provenance": { "deposit_id": "9EBS", "doi": "10.1158/1535-7163.MCT-24-0515", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9EBS" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of USP1-UAF1-Ubiquitin in complex with TNG348" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains U)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8B3I", "evidence_id": "EV-PDB-8B3I-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.5 }, "provenance": { "deposit_id": "8B3I", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8B3I" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "CRL4CSA-E2-Ub (state 2)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "GOL", "PE8", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains E)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/8AMS", "evidence_id": "EV-PDB-8AMS-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.4 }, "provenance": { "deposit_id": "8AMS", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/8AMS" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CA" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C,Ub-fused CBLock peptide (chains B,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9ERZ", "evidence_id": "EV-PDB-9ERZ-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.02 }, "provenance": { "deposit_id": "9ERZ", "doi": "10.1016/j.ymthe.2025.04.042", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9ERZ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of CBL-TKBD bound to Ubiquitin-fused CBLock peptide" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "A1IB8", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9FCI", "evidence_id": "EV-PDB-9FCI-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.2 }, "provenance": { "deposit_id": "9FCI", "doi": "10.1021/acs.jmedchem.4c01184", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9FCI" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "USP1 bound to KSQ-4279 and ubiquitin conjugated to FANCD2 (focused refinement)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "JDA", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9FCJ", "evidence_id": "EV-PDB-9FCJ-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.7 }, "provenance": { "deposit_id": "9FCJ", "doi": "10.1021/acs.jmedchem.4c01184", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9FCJ" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "USP1 bound to ML323 and ubiquitin conjugated to FANCD2 (ordered subset, focused refinement)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "A1IDH" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9FJ3", "evidence_id": "EV-PDB-9FJ3-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.4 }, "provenance": { "deposit_id": "9FJ3", "doi": "10.1039/d4sc04204b", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9FJ3" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of ubiquitin bound of coiled-coil UIM form 2" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "A1IDH" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9FJ4", "evidence_id": "EV-PDB-9FJ4-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.54 }, "provenance": { "deposit_id": "9FJ4", "doi": "10.1039/d4sc04204b", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9FJ4" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of ubiquitin bound to coiled coil-UIM form 1" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SY8" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9GKN", "evidence_id": "EV-PDB-9GKN-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.4 }, "provenance": { "deposit_id": "9GKN", "doi": "10.1038/s41594-025-01561-1", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9GKN" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Structure of HECT E3 TRIP12 forming K29-linked Ubiquitin chains" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SY8" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9GKN", "evidence_id": "EV-PDB-9GKN-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.4 }, "provenance": { "deposit_id": "9GKN", "doi": "10.1038/s41594-025-01561-1", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9GKN" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Structure of HECT E3 TRIP12 forming K29-linked Ubiquitin chains" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-B (chains D)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9HNW", "evidence_id": "EV-PDB-9HNW-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.04 }, "provenance": { "deposit_id": "9HNW", "doi": "10.1038/s41467-025-61768-0", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9HNW" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "USP1-UAF1 bound to Lys63-linked diubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-B (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9HNW", "evidence_id": "EV-PDB-9HNW-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.04 }, "provenance": { "deposit_id": "9HNW", "doi": "10.1038/s41467-025-61768-0", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9HNW" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "USP1-UAF1 bound to Lys63-linked diubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SRE" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -193.15 }, "construct": { "description": "Ubiquitin (chains B,D,F,H)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9IJU", "evidence_id": "EV-PDB-9IJU-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.46 }, "provenance": { "deposit_id": "9IJU", "doi": "10.1021/acs.jmedchem.5c00032", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9IJU" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SAM", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9ISZ", "evidence_id": "EV-PDB-9ISZ-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.6 }, "provenance": { "deposit_id": "9ISZ", "doi": "10.1126/sciadv.adu1864", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9ISZ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin K29C (chains D)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9KEN", "evidence_id": "EV-PDB-9KEN-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.63 }, "provenance": { "deposit_id": "9KEN", "doi": "10.1038/s41467-025-59569-6", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9KEN" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "cryo-EM structure of TRIP12 in complex with K29/48 branched-triUb" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9KEN", "evidence_id": "EV-PDB-9KEN-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.63 }, "provenance": { "deposit_id": "9KEN", "doi": "10.1038/s41467-025-59569-6", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9KEN" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "cryo-EM structure of TRIP12 in complex with K29/48 branched-triUb" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9KHS", "evidence_id": "EV-PDB-9KHS-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 4.31 }, "provenance": { "deposit_id": "9KHS", "doi": "10.1038/s41589-025-01985-2", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9KHS" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb (monomeric conformation)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains E)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9KHS", "evidence_id": "EV-PDB-9KHS-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 4.31 }, "provenance": { "deposit_id": "9KHS", "doi": "10.1038/s41589-025-01985-2", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9KHS" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb (monomeric conformation)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains D)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9KHS", "evidence_id": "EV-PDB-9KHS-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 4.31 }, "provenance": { "deposit_id": "9KHS", "doi": "10.1038/s41589-025-01985-2", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9KHS" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb (monomeric conformation)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9M7O", "evidence_id": "EV-PDB-9M7O-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 4.14 }, "provenance": { "deposit_id": "9M7O", "doi": "10.1038/s41589-025-01985-2", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9M7O" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of Ufd2/Ubc4-ub complex with K29triUb(monomeric conformation)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains E)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9M7O", "evidence_id": "EV-PDB-9M7O-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 4.14 }, "provenance": { "deposit_id": "9M7O", "doi": "10.1038/s41589-025-01985-2", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9M7O" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of Ufd2/Ubc4-ub complex with K29triUb(monomeric conformation)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains D)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9M7O", "evidence_id": "EV-PDB-9M7O-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 4.14 }, "provenance": { "deposit_id": "9M7O", "doi": "10.1038/s41589-025-01985-2", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9M7O" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of Ufd2/Ubc4-ub complex with K29triUb(monomeric conformation)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AMP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9MC5", "evidence_id": "EV-PDB-9MC5-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.29 }, "provenance": { "deposit_id": "9MC5", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9MC5" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 3" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9N1F", "evidence_id": "EV-PDB-9N1F-4", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.1 }, "provenance": { "deposit_id": "9N1F", "doi": "10.1016/j.jmb.2025.169259", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9N1F" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal Structure of the Ark2C-Ubc13~Ub-Mms2 complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ADP", "ATP", "MG", "SPD", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains 2)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9OFV", "evidence_id": "EV-PDB-9OFV-54", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.16 }, "provenance": { "deposit_id": "9OFV", "doi": "10.1038/s41467-025-61235-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9OFV" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 6.4, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9PL1", "evidence_id": "EV-PDB-9PL1-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "9PL1", "doi": "10.1073/pnas.2519493122", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9PL1" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Structure of metastable folding intermediate of V17A/V26A ubiquitin derived from pressure-jump NMR data" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9PLQ", "evidence_id": "EV-PDB-9PLQ-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.19 }, "provenance": { "deposit_id": "9PLQ", "doi": "10.1016/j.molcel.2026.08.016", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9PLQ" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "HUWE1(CS)-Ubiquitin bound to the HECT domain" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.6, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin-40S ribosomal protein S27a (chains F,G)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9Q8Y", "evidence_id": "EV-PDB-9Q8Y-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.63 }, "provenance": { "deposit_id": "9Q8Y", "doi": "10.26508/lsa.202503394", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9Q8Y" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of RNF38 RING with linchpin mutant R454Y in complex with Ubch5B-Ub" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AMP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains C,E)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9QGG", "evidence_id": "EV-PDB-9QGG-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.58 }, "provenance": { "deposit_id": "9QGG", "doi": "10.1038/s41594-025-01717-z", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9QGG" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Consensus structure of dUBA1-UbDha-dBIRC6 trapped ternary complex" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AMP", "IHP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains C,E)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9QIA", "evidence_id": "EV-PDB-9QIA-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 4.38 }, "provenance": { "deposit_id": "9QIA", "doi": "10.1038/s41594-025-01717-z", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9QIA" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Structure of UBA6-UbDha-BIRC6 trapped ternary complex (cluster 2)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "SY8", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains U)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SDX", "evidence_id": "EV-PDB-9SDX-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.97 }, "provenance": { "deposit_id": "9SDX", "doi": "10.1073/pnas.2524899122", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SDX" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains K,M)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SMN", "evidence_id": "EV-PDB-9SMN-6", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.2 }, "provenance": { "deposit_id": "9SMN", "doi": "10.1038/s41467-026-75797-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SMN" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BRCA1-A complex bound to K63-polyUbATA - open form StateC StateP" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains L,N)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SMN", "evidence_id": "EV-PDB-9SMN-7", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.2 }, "provenance": { "deposit_id": "9SMN", "doi": "10.1038/s41467-026-75797-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SMN" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BRCA1-A complex bound to K63-polyUbATA - open form StateC StateP" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains S,T,U,V)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SMN", "evidence_id": "EV-PDB-9SMN-8", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.2 }, "provenance": { "deposit_id": "9SMN", "doi": "10.1038/s41467-026-75797-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SMN" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BRCA1-A complex bound to K63-polyUbATA - open form StateC StateP" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains K,M)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SMP", "evidence_id": "EV-PDB-9SMP-6", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.0 }, "provenance": { "deposit_id": "9SMP", "doi": "10.1038/s41467-026-75797-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SMP" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BRCA1-A complex bound to K63-polyUbATA - open form double State P" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains L)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SMP", "evidence_id": "EV-PDB-9SMP-7", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.0 }, "provenance": { "deposit_id": "9SMP", "doi": "10.1038/s41467-026-75797-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SMP" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BRCA1-A complex bound to K63-polyUbATA - open form double State P" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains N)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SMP", "evidence_id": "EV-PDB-9SMP-8", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.0 }, "provenance": { "deposit_id": "9SMP", "doi": "10.1038/s41467-026-75797-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SMP" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BRCA1-A complex bound to K63-polyUbATA - open form double State P" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains S,T,U,V)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SMP", "evidence_id": "EV-PDB-9SMP-9", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.0 }, "provenance": { "deposit_id": "9SMP", "doi": "10.1038/s41467-026-75797-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SMP" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BRCA1-A complex bound to K63-polyUbATA - open form double State P" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains S)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SMS", "evidence_id": "EV-PDB-9SMS-5", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.3 }, "provenance": { "deposit_id": "9SMS", "doi": "10.1038/s41467-026-75797-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SMS" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BRCA1-A complex: Ubiquitin bound to BRE at the wrist site (focused 3D class)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "A1JPL", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains L,N)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SNA", "evidence_id": "EV-PDB-9SNA-6", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.2 }, "provenance": { "deposit_id": "9SNA", "doi": "10.1038/s41467-026-75797-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SNA" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BRCA1-A complex bound to K63-diUbATA - open form StateC StateP" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "A1JPL", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains K,M)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SNA", "evidence_id": "EV-PDB-9SNA-7", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.2 }, "provenance": { "deposit_id": "9SNA", "doi": "10.1038/s41467-026-75797-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SNA" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BRCA1-A complex bound to K63-diUbATA - open form StateC StateP" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "A1JPL", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains S,T)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SNA", "evidence_id": "EV-PDB-9SNA-8", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.2 }, "provenance": { "deposit_id": "9SNA", "doi": "10.1038/s41467-026-75797-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SNA" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BRCA1-A complex bound to K63-diUbATA - open form StateC StateP" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains L)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SO9", "evidence_id": "EV-PDB-9SO9-6", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.4 }, "provenance": { "deposit_id": "9SO9", "doi": "10.1038/s41467-026-75797-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SO9" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BRCA1-A complex bound to K63-oligoUbATA - closed form StateC*" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains M)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SO9", "evidence_id": "EV-PDB-9SO9-7", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.4 }, "provenance": { "deposit_id": "9SO9", "doi": "10.1038/s41467-026-75797-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SO9" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BRCA1-A complex bound to K63-oligoUbATA - closed form StateC*" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains N)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SO9", "evidence_id": "EV-PDB-9SO9-8", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.4 }, "provenance": { "deposit_id": "9SO9", "doi": "10.1038/s41467-026-75797-w", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SO9" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "BRCA1-A complex bound to K63-oligoUbATA - closed form StateC*" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains G,H)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SQV", "evidence_id": "EV-PDB-9SQV-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.21 }, "provenance": { "deposit_id": "9SQV", "doi": "10.1038/s41467-026-75795-y", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SQV" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Composite map)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains G,H,I,J)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SQW", "evidence_id": "EV-PDB-9SQW-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.2 }, "provenance": { "deposit_id": "9SQW", "doi": "10.1038/s41467-026-75795-y", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SQW" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of the ARISCdC(E33A):K63-Ub7 complex (Composite map)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains K,L,M,N,O,P)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SQY", "evidence_id": "EV-PDB-9SQY-5", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.92 }, "provenance": { "deposit_id": "9SQY", "doi": "10.1038/s41467-026-75795-y", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SQY" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of the ARISC(E33A)-RAP80:K63-Ub7 complex (Composite map)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "COA", "GTP", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin-60S ribosomal protein L40 (chains LD)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9SYR", "evidence_id": "EV-PDB-9SYR-72", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.55 }, "provenance": { "deposit_id": "9SYR", "doi": "10.1126/sciadv.aeb1017", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9SYR" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Human quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatD" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "FE", "SY8", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains U)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9T7V", "evidence_id": "EV-PDB-9T7V-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.95 }, "provenance": { "deposit_id": "9T7V", "doi": "10.1038/s41467-026-72524-3", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9T7V" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "A1EQF" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.5, "salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + NMR restraints", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9UV6", "evidence_id": "EV-PDB-9UV6-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "structure", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "9UV6", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9UV6" }, "reader": null, "source_kind": "deposit", "technique": "nmr_structure", "title": "Encounter complex structure of E2N and Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "A1EY9", "GOL", "NI" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains F,H)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9WYW", "evidence_id": "EV-PDB-9WYW-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.2 }, "provenance": { "deposit_id": "9WYW", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9WYW" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of K27-linked di-ubiquitin in complex with synthetic antigen binding fragment" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.5, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9YEA", "evidence_id": "EV-PDB-9YEA-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.83 }, "provenance": { "deposit_id": "9YEA", "doi": "10.1016/j.bbrc.2025.152873", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9YEA" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Structure of the isopeptide bond-linked UbcH5b~Ubiquitin conjugate complex for an M1K/C85K UbcH5b mutant" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "IHP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains B,D)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9YKW", "evidence_id": "EV-PDB-9YKW-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": 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"data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9YLF", "evidence_id": "EV-PDB-9YLF-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.14 }, "provenance": { "deposit_id": "9YLF", "doi": "10.1038/s41467-026-69882-3", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9YLF" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of single-loaded human UBA6-UBE2Z/Ub(a) adenylate complex." }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "IMD", "ZN" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9VVV", "evidence_id": "EV-PDB-9VVV-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.304 }, "provenance": { "deposit_id": "9VVV", "doi": "10.1038/s42003-026-10386-7", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9VVV" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of USP15 catalytic domain in complex with Ub-PA" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AYE" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Ubiquitin (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9R85", "evidence_id": "EV-PDB-9R85-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.04 }, "provenance": { "deposit_id": "9R85", "doi": "10.1038/s41467-026-69520-y", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9R85" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of the E3 ligase HECTD3 conjugated to ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AMP", "IHP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains C,E)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9QH5", "evidence_id": "EV-PDB-9QH5-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.09 }, "provenance": { "deposit_id": "9QH5", "doi": "10.1038/s41594-025-01717-z", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9QH5" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Consensus structure of UBA6-UbDha-BIRC6 trapped ternary complex (doubly loaded)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "ATP", "IHP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9QGW", "evidence_id": "EV-PDB-9QGW-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.62 }, "provenance": { "deposit_id": "9QGW", "doi": "10.1038/s41594-025-01717-z", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9QGW" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Consensus structure of UBA6-UbDha-BIRC6 trapped ternary complex (singly loaded)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AMP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains C,E)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9QGR", "evidence_id": "EV-PDB-9QGR-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.1 }, "provenance": { "deposit_id": "9QGR", "doi": "10.1038/s41594-025-01717-z", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9QGR" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Structure of dUBA1-UbDha-dBIRC6 trapped ternary complex (Cluster 4)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AMP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains C,E)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9QGI", "evidence_id": "EV-PDB-9QGI-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.16 }, "provenance": { "deposit_id": "9QGI", "doi": "10.1038/s41594-025-01717-z", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9QGI" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Structure of dUBA1-UbDha-dBIRC6 trapped ternary complex (Cluster 2)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "CD", "CL" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9OVX", "evidence_id": "EV-PDB-9OVX-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.5 }, "provenance": { "deposit_id": "9OVX", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9OVX" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "CRYSTAL STRUCTURE OF UBIQUITIN K27M MUTANT" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "6NA" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Polyubiquitin-C (chains C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9O4M", "evidence_id": "EV-PDB-9O4M-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.0 }, "provenance": { "deposit_id": "9O4M", "doi": "10.1002/cbic.202500318", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9O4M" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Crystal structure of Ubiquitin Carboxy Terminal Hydrolase L1 Q209C mutant covalently crosslinked to ubiquitin genetically encoded with N6-(6-bromohexanoyl)-L-lysine" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "AMP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains C)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9MC4", "evidence_id": "EV-PDB-9MC4-3", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 3.32 }, "provenance": { "deposit_id": "9MC4", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9MC4" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 4" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C (chains D,d)", "labels": [] }, "data_format": "mmCIF + EMDB map", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9KHT", "evidence_id": "EV-PDB-9KHT-1", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": "ub-structures-folded", "state_id": "Ub-folded", "who": "rule:ub-structures-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 4.85 }, "provenance": { "deposit_id": "9KHT", "doi": "10.1038/s41589-025-01985-2", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/9KHT" }, "reader": null, "source_kind": "deposit", "technique": "cryoem", "title": "cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked triUb (dimeric conformation)" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "XB7" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "Ubiquitin (chains B,D,F,H)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/9IML", "evidence_id": "EV-PDB-9IML-2", "mappings": [ { "confidence": "medium", "justification": "Experimental structure containing ubiquitin; free and bound ubiquitin keep the native fold unless the title says otherwise.", "rule": 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"salt_mM": null, "temperature_c": 24.85 }, "construct": { "description": "BMRB data: 13C chemical shifts, 15N chemical shifts, 1H chemical shifts", "labels": [] }, "data_format": "NMR-STAR", "data_level": "processed", "data_link": "https://bmrb.io/data_library/summary/index.php?bmrbId=53268", "evidence_id": "EV-BMRB-53268", "mappings": [ { "confidence": "low", "justification": "NMR shift or relaxation entry for ubiquitin under native conditions.", "rule": "ub-nmr-folded", "state_id": "Ub-folded", "who": "rule:ub-nmr-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "chemical_shift", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "bmr53268", "doi": "10.13018/BMR53268", "licence": "CC0 1.0 (verify)", "retrieved": "2026-10-19", "source": "BMRB", "url": "https://bmrb.io/data_library/summary/index.php?bmrbId=53268" }, "reader": null, "source_kind": "deposit", "technique": "nmr_shifts", "title": "Ubiquitin V17A/V26A retracted Intermediate" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "From the first sample condition list of the entry.", "ph": 5.0, "salt_mM": null, "temperature_c": 19.85 }, "construct": { "description": "BMRB data: 1H chemical shifts, 13C chemical shifts, 15N chemical shifts", "labels": [] }, "data_format": "NMR-STAR", "data_level": "processed", "data_link": "https://bmrb.io/data_library/summary/index.php?bmrbId=5387", "evidence_id": "EV-BMRB-5387", "mappings": [ { "confidence": "low", "justification": "NMR shift or relaxation entry for ubiquitin under native conditions.", "rule": "ub-nmr-folded", "state_id": "Ub-folded", "who": "rule:ub-nmr-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "chemical_shift", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "bmr5387", "doi": "10.13018/BMR5387", "licence": "CC0 1.0 (verify)", "retrieved": "2026-10-19", "source": "BMRB", "url": "https://bmrb.io/data_library/summary/index.php?bmrbId=5387" }, "reader": null, "source_kind": "deposit", "technique": "nmr_shifts", "title": "Complete 1H, 13C, and 15N chemical shifts for human recombinant ubiquitin in reverse micelles" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "From the first sample condition list of the entry.", "ph": 6.6, "salt_mM": null, "temperature_c": 18.85 }, "construct": { "description": "BMRB data: 13C chemical shifts, 15N chemical shifts, 1H chemical shifts", "labels": [] }, "data_format": "NMR-STAR", "data_level": "processed", "data_link": "https://bmrb.io/data_library/summary/index.php?bmrbId=6457", "evidence_id": "EV-BMRB-6457", "mappings": [ { "confidence": "low", "justification": "NMR shift or relaxation entry for ubiquitin under native conditions.", "rule": "ub-nmr-folded", "state_id": "Ub-folded", "who": "rule:ub-nmr-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "chemical_shift", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "bmr6457", "doi": "10.13018/BMR6457", "licence": "CC0 1.0 (verify)", "retrieved": "2026-10-19", "source": "BMRB", "url": "https://bmrb.io/data_library/summary/index.php?bmrbId=6457" }, "reader": null, "source_kind": "deposit", "technique": "nmr_shifts", "title": "Validation of Protein Structure from Anisotropic Carbonyl Chemical Shifts in a Dilute Liquid Crystalline Phase" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "From the first sample condition list of the entry.", "ph": null, "salt_mM": null, "temperature_c": 29.85 }, "construct": { "description": "BMRB data: 13C chemical shifts, 15N chemical shifts, 1H chemical shifts, order parameters, T1 relaxation values", "labels": [] }, "data_format": "NMR-STAR", "data_level": "processed", "data_link": 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the entry.", "ph": 4.7, "salt_mM": null, "temperature_c": 26.85 }, "construct": { "description": "BMRB data: heteronuclear NOE values, T1 relaxation values, T2 relaxation values, order parameters", "labels": [] }, "data_format": "NMR-STAR", "data_level": "processed", "data_link": "https://bmrb.io/data_library/summary/index.php?bmrbId=6470", "evidence_id": "EV-BMRB-6470", "mappings": [ { "confidence": "low", "justification": "NMR shift or relaxation entry for ubiquitin under native conditions.", "rule": "ub-nmr-folded", "state_id": "Ub-folded", "who": "rule:ub-nmr-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "relaxation_rate", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "bmr6470", "doi": "10.13018/BMR6470", "licence": "CC0 1.0 (verify)", "retrieved": "2026-10-19", "source": "BMRB", "url": "https://bmrb.io/data_library/summary/index.php?bmrbId=6470" }, "reader": null, "source_kind": "deposit", "technique": "nmr_dynamics", "title": "Rotational Diffusion Anisotropy of Human Ubiquitin from 15N NMR Relaxation" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "From the first sample condition list of the entry.", "ph": 4.7, "salt_mM": null, "temperature_c": 49.85 }, "construct": { "description": "BMRB data: 1H chemical shifts", "labels": [] }, "data_format": "NMR-STAR", "data_level": "processed", "data_link": "https://bmrb.io/data_library/summary/index.php?bmrbId=68", "evidence_id": "EV-BMRB-68", "mappings": [ { "confidence": "low", "justification": "NMR shift or relaxation entry for ubiquitin under native conditions.", "rule": "ub-nmr-folded", "state_id": "Ub-folded", "who": "rule:ub-nmr-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "chemical_shift", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "bmr68", "doi": "10.13018/BMR68", "licence": "CC0 1.0 (verify)", "retrieved": "2026-10-19", "source": "BMRB", "url": "https://bmrb.io/data_library/summary/index.php?bmrbId=68" }, "reader": null, "source_kind": "deposit", "technique": "nmr_shifts", "title": "Sequential 1H NMR Assignments and Secondary Structure Identification of Human Ubiquitin" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "From the first sample condition list of the entry.", "ph": 4.0, "salt_mM": null, "temperature_c": -5.15 }, "construct": { "description": "BMRB data: 13C chemical shifts, 15N chemical shifts", "labels": [] }, "data_format": "NMR-STAR", "data_level": "processed", "data_link": "https://bmrb.io/data_library/summary/index.php?bmrbId=7111", "evidence_id": "EV-BMRB-7111", "mappings": [ { "confidence": "low", "justification": "NMR shift or relaxation entry for ubiquitin under native conditions.", "rule": "ub-nmr-folded", "state_id": "Ub-folded", "who": "rule:ub-nmr-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "chemical_shift", "uncertainty": null, "unit": null, "value": null }, "provenance": { "deposit_id": "bmr7111", "doi": "10.13018/BMR7111", "licence": "CC0 1.0 (verify)", "retrieved": "2026-10-19", "source": "BMRB", "url": "https://bmrb.io/data_library/summary/index.php?bmrbId=7111" }, "reader": null, "source_kind": "deposit", "technique": "nmr_shifts", "title": "Chemical shift assignment of multicrystalline ubiquitin using solid state MAS NMR spectroscopy" }, { "conditions": { "applied_force_pn": null, "buffer": "20 mM HEPES 200 mM NaCl 0.01 mM ZnSO4 1 mM DTT", "environment": "in_vitro", "ions": [], "ligands": [ "partner: E3 ubiquitin-protein ligase RNF8", "partner: Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A)" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 18.85 nm.", "ph": 6.8, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C with E3 ubiquitin-protein ligase RNF8, Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A)", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDBR3/", "evidence_id": "EV-SASBDB-SASDBR3", "mappings": [], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": null, "unit": "nm", "value": 4.45 }, "provenance": { "deposit_id": "SASDBR3", "doi": "10.1074/jbc.M116.715698", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDBR3/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment." }, { "conditions": { "applied_force_pn": null, "buffer": "20 mM HEPES 200 mM NaCl 0.01 mM ZnSO4 1 mM DTT", "environment": "in_vitro", "ions": [], "ligands": [ "partner: E3 ubiquitin-protein ligase RNF8", "partner: Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A)", "partner: Ubiquitin-conjugating enzyme E2 variant 2" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 23.8 nm.", "ph": 6.8, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C with E3 ubiquitin-protein ligase RNF8, Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A), Ubiquitin-conjugating enzyme E2 variant 2", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDBS3/", "evidence_id": "EV-SASBDB-SASDBS3", "mappings": [], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": 0.21, "unit": "nm", "value": 5.38 }, "provenance": { "deposit_id": "SASDBS3", "doi": "10.1074/jbc.M116.715698", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDBS3/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment." }, { "conditions": { "applied_force_pn": null, "buffer": "20 mM HEPES 200 mM NaCl 0.01 mM ZnSO4 1 mM DTT", "environment": "in_vitro", "ions": [], "ligands": [ "partner: E3 ubiquitin-protein ligase RNF8 mutant (L451D)", "partner: Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A)" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 18.94 nm.", "ph": 6.8, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C with Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A), E3 ubiquitin-protein ligase RNF8 mutant (L451D)", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDBT3/", "evidence_id": "EV-SASBDB-SASDBT3", "mappings": [], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": null, "unit": "nm", "value": 4.28 }, "provenance": { "deposit_id": "SASDBT3", "doi": "10.1074/jbc.M116.715698", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDBT3/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment." }, { "conditions": { "applied_force_pn": null, "buffer": "20 mM HEPES 200 mM NaCl 0.01 mM ZnSO4 1 mM DTT", "environment": "in_vitro", "ions": [], "ligands": [ "partner: E3 ubiquitin-protein ligase RNF8 mutant (L451D)", "partner: Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A)", "partner: Ubiquitin-conjugating enzyme E2 variant 2" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 23.8 nm.", "ph": 6.8, "salt_mM": null, "temperature_c": null }, "construct": { "description": "Polyubiquitin-C with Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A), Ubiquitin-conjugating enzyme E2 variant 2, E3 ubiquitin-protein ligase RNF8 mutant (L451D)", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDBU3/", "evidence_id": "EV-SASBDB-SASDBU3", "mappings": [], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": null, "unit": "nm", "value": 5.19 }, "provenance": { "deposit_id": "SASDBU3", "doi": "10.1074/jbc.M116.715698", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDBU3/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment." }, { "conditions": { "applied_force_pn": null, "buffer": "20mM HEPES, 150mM NaCl", "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 7 nm.", "ph": 7.4, "salt_mM": null, "temperature_c": 25.0 }, "construct": { "description": "Polyubiquitin-C", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDCG7/", "evidence_id": "EV-SASBDB-SASDCG7", "mappings": [ { "confidence": "low", "justification": "SAXS of ubiquitin alone under native conditions; samples with partners are excluded.", "rule": "ub-saxs-folded", "state_id": "Ub-folded", "who": "rule:ub-saxs-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": 0.15, "unit": "nm", "value": 2.0 }, "provenance": { "deposit_id": "SASDCG7", "doi": "10.1021/acs.biochem.7b00817", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDCG7/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "Characterizing Protein Dynamics with Integrative Use of Bulk and Single-Molecule Techniques." }, { "conditions": { "applied_force_pn": null, "buffer": "100mM NaCl, 10mM sodium acetate", "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 6.5 nm.", "ph": 6.0, "salt_mM": null, "temperature_c": 25.0 }, "construct": { "description": "Polyubiquitin-C", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDCL6/", "evidence_id": "EV-SASBDB-SASDCL6", "mappings": [ { "confidence": "low", "justification": "SAXS of ubiquitin alone under native conditions; samples with partners are excluded.", "rule": "ub-saxs-folded", "state_id": "Ub-folded", "who": "rule:ub-saxs-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": 0.01, "unit": "nm", "value": 2.084 }, "provenance": { "deposit_id": "SASDCL6", "doi": "10.7554/eLife.05767", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDCL6/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition." }, { "conditions": { "applied_force_pn": null, "buffer": "20 mM HEPES, 100 mM NaCl, 5 mM DTT", "environment": "in_vitro", "ions": [], "ligands": [ "partner: Ubiquitin carboxyl-terminal hydrolase MINDY-2" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 6.8 nm.", "ph": 7.5, "salt_mM": null, "temperature_c": 20.0 }, "construct": { "description": "Polyubiquitin-C with Ubiquitin carboxyl-terminal hydrolase MINDY-2", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDJA3/", "evidence_id": "EV-SASBDB-SASDJA3", "mappings": [], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": 0.05, "unit": "nm", "value": 2.31 }, "provenance": { "deposit_id": "SASDJA3", "doi": "10.1016/j.molcel.2021.08.024", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDJA3/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2." }, { "conditions": { "applied_force_pn": null, "buffer": "20 mM HEPES, 100 mM NaCl, 5 mM DTT", "environment": "in_vitro", "ions": [], "ligands": [ "partner: Ubiquitin carboxyl-terminal hydrolase C266A mutant" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 8 nm.", "ph": 7.5, "salt_mM": null, "temperature_c": 20.0 }, "construct": { "description": "Polyubiquitin-C with Ubiquitin carboxyl-terminal hydrolase C266A mutant", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDJB3/", "evidence_id": "EV-SASBDB-SASDJB3", "mappings": [], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": 0.01, "unit": "nm", "value": 2.51 }, "provenance": { "deposit_id": "SASDJB3", "doi": "10.1016/j.molcel.2021.08.024", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDJB3/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2." }, { "conditions": { "applied_force_pn": null, "buffer": "20 mM HEPES, 100 mM NaCl, 5 mM DTT", "environment": "in_vitro", "ions": [], "ligands": [ "partner: Ubiquitin carboxyl-terminal hydrolase C266A mutant" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 8.77 nm.", "ph": 7.5, "salt_mM": null, "temperature_c": 20.0 }, "construct": { "description": "Polyubiquitin-C with Ubiquitin carboxyl-terminal hydrolase C266A mutant", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDJC3/", "evidence_id": "EV-SASBDB-SASDJC3", "mappings": [], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": 0.01, "unit": "nm", "value": 2.83 }, "provenance": { "deposit_id": "SASDJC3", "doi": "10.1016/j.molcel.2021.08.024", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDJC3/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2." }, { "conditions": { "applied_force_pn": null, "buffer": "20 mM HEPES, 100 mM NaCl, 5 mM DTT", "environment": "in_vitro", "ions": [], "ligands": [ "partner: Ubiquitin carboxyl-terminal hydrolase C266A mutant" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 9.2 nm.", "ph": 7.5, "salt_mM": null, "temperature_c": 20.0 }, "construct": { "description": "Polyubiquitin-C with Ubiquitin carboxyl-terminal hydrolase C266A mutant", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDJD3/", "evidence_id": "EV-SASBDB-SASDJD3", "mappings": [], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": null, "unit": "nm", "value": 2.88 }, "provenance": { "deposit_id": "SASDJD3", "doi": "10.1016/j.molcel.2021.08.024", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDJD3/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2." }, { "conditions": { "applied_force_pn": null, "buffer": "20 mM HEPES, 100 mM NaCl, 5 mM DTT", "environment": "in_vitro", "ions": [], "ligands": [ "partner: Ubiquitin carboxyl-terminal hydrolase C266A mutant" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 9 nm.", "ph": 7.5, "salt_mM": null, "temperature_c": 20.0 }, "construct": { "description": "Polyubiquitin-C with Ubiquitin carboxyl-terminal hydrolase C266A mutant", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDJE3/", "evidence_id": "EV-SASBDB-SASDJE3", "mappings": [], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": 0.02, "unit": "nm", "value": 2.8 }, "provenance": { "deposit_id": "SASDJE3", "doi": "10.1016/j.molcel.2021.08.024", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDJE3/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2." }, { "conditions": { "applied_force_pn": null, "buffer": "50 mM Tris, 150 mM NaCl, 1 mM TCEP", "environment": "in_vitro", "ions": [], "ligands": [ "partner: Ubiquitin-conjugating enzyme E2 D1 (S22R, C85K, D87S)" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 7.4 nm.", "ph": 8.0, "salt_mM": null, "temperature_c": 10.0 }, "construct": { "description": "Ubiquitin with Ubiquitin-conjugating enzyme E2 D1 (S22R, C85K, D87S)", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDP34/", "evidence_id": "EV-SASBDB-SASDP34", "mappings": [], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": 0.371, "unit": "nm", "value": 2.094 }, "provenance": { "deposit_id": "SASDP34", "doi": "10.1007/s00249-022-01620-1", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDP34/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "Production and characterisation of modularly deuterated UBE2D1–Ub conjugate by small angle neutron and X-ray scattering" }, { "conditions": { "applied_force_pn": null, "buffer": "20 mM HEPES, 100 mM NaCl", "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 6.48 nm.", "ph": 7.0, "salt_mM": null, "temperature_c": 20.0 }, "construct": { "description": "Polyubiquitin-C", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDSF2/", "evidence_id": "EV-SASBDB-SASDSF2", "mappings": [ { "confidence": "low", "justification": "SAXS of ubiquitin alone under native conditions; samples with partners are excluded.", "rule": "ub-saxs-folded", "state_id": "Ub-folded", "who": "rule:ub-saxs-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": 0.086, "unit": "nm", "value": 1.947 }, "provenance": { "deposit_id": "SASDSF2", "doi": "10.1039/d3dt01815f", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDSF2/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "Stretching the chains: the destabilizing impact of Cu(2+) and Zn(2+) ions on K48-linked diubiquitin." }, { "conditions": { "applied_force_pn": null, "buffer": "20 mM HEPES, 100 mM NaCl", "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 7.49 nm.", "ph": 7.0, "salt_mM": null, "temperature_c": 20.0 }, "construct": { "description": "Polyubiquitin-C", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDSG2/", "evidence_id": "EV-SASBDB-SASDSG2", "mappings": [ { "confidence": "low", "justification": "SAXS of ubiquitin alone under native conditions; samples with partners are excluded.", "rule": "ub-saxs-folded", "state_id": "Ub-folded", "who": "rule:ub-saxs-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": 0.226, "unit": "nm", "value": 1.995 }, "provenance": { "deposit_id": "SASDSG2", "doi": "10.1039/d3dt01815f", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDSG2/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "Stretching the chains: the destabilizing impact of Cu(2+) and Zn(2+) ions on K48-linked diubiquitin." }, { "conditions": { "applied_force_pn": null, "buffer": "20 mM HEPES, 100 mM NaCl", "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 6.29 nm.", "ph": 7.0, "salt_mM": null, "temperature_c": 20.0 }, "construct": { "description": "Polyubiquitin-C", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDSH2/", "evidence_id": "EV-SASBDB-SASDSH2", "mappings": [ { "confidence": "low", "justification": "SAXS of ubiquitin alone under native conditions; samples with partners are excluded.", "rule": "ub-saxs-folded", "state_id": "Ub-folded", "who": "rule:ub-saxs-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "radius_of_gyration", "uncertainty": 0.209, "unit": "nm", "value": 1.923 }, "provenance": { "deposit_id": "SASDSH2", "doi": "10.1039/d3dt01815f", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDSH2/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "Stretching the chains: the destabilizing impact of Cu(2+) and Zn(2+) ions on K48-linked diubiquitin." }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_silico", "ions": [], "ligands": [], "notes": "Computed prediction; no experimental conditions.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "AlphaFold Monomer v2.0 pipeline, residues 1-685", "labels": [] }, "data_format": "mmCIF, PAE JSON", "data_level": "processed", "data_link": "https://alphafold.ebi.ac.uk/entry/P0CG48", "evidence_id": "EV-AFDB-AF-P0CG48-F1", "mappings": [ { "confidence": "low", "justification": "AlphaFold prediction of the native fold (prediction).", "rule": "ub-af-folded", "state_id": "Ub-folded", "who": "rule:ub-af-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "plddt", "uncertainty": null, "unit": "pLDDT", "value": 88.62 }, "provenance": { "deposit_id": "AF-P0CG48-F1", "doi": null, "licence": "CC BY 4.0", "retrieved": "2026-10-19", "source": "AlphaFold DB", "url": "https://alphafold.ebi.ac.uk/entry/P0CG48" }, "reader": null, "source_kind": "computed", "technique": "af_prediction", "title": "AlphaFold DB prediction AF-P0CG48-F1" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_silico", "ions": [], "ligands": [], "notes": "Simulation; temperature is the thermostat setting.", "ph": null, "salt_mM": null, "temperature_c": 26.85 }, "construct": { "description": "start 1UBI; Amber Parm99", "labels": [] }, "data_format": "trajectory", "data_level": "processed", "data_link": "https://mmb.mddbr.eu/#/id/A013P/overview", "evidence_id": "EV-MDDB-A013P", "mappings": [ { "confidence": "low", "justification": "Simulation started from a native ubiquitin structure (prediction).", "rule": "ub-md-folded", "state_id": "Ub-folded", "who": "rule:ub-md-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "trajectory", "uncertainty": null, "unit": "ns", "value": 10.0 }, "provenance": { "deposit_id": "A013P", "doi": "10.1016/j.str.2010.07.013", "licence": "This trajectory dataset is released under a Creative Commons Attribution 4.0 International Public License", "retrieved": "2026-10-19", "source": "MDDB", "url": "https://mmb.mddbr.eu/#/id/A013P/overview" }, "reader": null, "source_kind": "computed", "technique": "md", "title": "MoDEL 1UBI" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_silico", "ions": [], "ligands": [], "notes": "Simulation; temperature is the thermostat setting.", "ph": null, "salt_mM": null, "temperature_c": 26.85 }, "construct": { "description": "start 1UBQ; Amber Parm99", "labels": [] }, "data_format": "trajectory", "data_level": "processed", "data_link": "https://mmb.mddbr.eu/#/id/A0142/overview", "evidence_id": "EV-MDDB-A0142", "mappings": [ { "confidence": "low", "justification": "Simulation started from a native ubiquitin structure (prediction).", "rule": "ub-md-folded", "state_id": "Ub-folded", "who": "rule:ub-md-folded" } ], "molecule_id": "P0CG48", "observable": { "type": "trajectory", "uncertainty": null, "unit": "ns", "value": 10.0 }, "provenance": { "deposit_id": "A0142", "doi": "10.1016/j.str.2010.07.013", "licence": "This trajectory dataset is released under a Creative Commons Attribution 4.0 International Public License", "retrieved": "2026-10-19", "source": "MDDB", "url": "https://mmb.mddbr.eu/#/id/A0142/overview" }, "reader": null, "source_kind": "computed", "technique": "md", "title": "MoDEL 1UBQ" } ], "models": [ { "assumptions": null, "basis": "observed", "constraints_used": [ "EV-PDB-1UBQ-1" ], "file": "models/P0CG48/Ub-folded.cif", "format": "mmCIF", "model_id": "Ub-folded-cif", "molecule_id": "P0CG48", "provenance": { "deposit_id": "1UBQ", "doi": "10.1016/0022-2836(87)90679-6", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://files.rcsb.org/download/1UBQ.cif" }, "state_id": "Ub-folded" }, { "assumptions": null, "basis": "observed", "constraints_used": [ "EV-PDB-1UBQ-1" ], "file": "models/P0CG48/Ub-folded.pdb", "format": "PDB", "model_id": "Ub-folded-pdb", "molecule_id": "P0CG48", "provenance": { "deposit_id": "1UBQ", "doi": "10.1016/0022-2836(87)90679-6", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://files.rcsb.org/download/1UBQ.pdb" }, "state_id": "Ub-folded" } ], "molecule": { "components": [], "domains": [ { "end": 76, "name": "Ubiquitin-like 1", "start": 1 }, { "end": 152, "name": "Ubiquitin-like 2", "start": 77 }, { "end": 228, "name": "Ubiquitin-like 3", "start": 153 }, { "end": 304, "name": "Ubiquitin-like 4", "start": 229 }, { "end": 380, "name": "Ubiquitin-like 5", "start": 305 }, { "end": 456, "name": "Ubiquitin-like 6", "start": 381 }, { "end": 532, "name": "Ubiquitin-like 7", "start": 457 }, { "end": 608, "name": "Ubiquitin-like 8", "start": 533 }, { "end": 684, "name": "Ubiquitin-like 9", "start": 609 } ], "gene": "UBC", "identifiers": { "genbank": null, "isoform": null, "nakb": null, "pdb": [], "rfam": null, "rnacentral": null, "uniprot": "P0CG48" }, "ligands": [], "modifications": [ { "kind": "ptm", "name": "Phosphoserine; by PINK1", "position": 65, "source": "UniProtKB" }, { "kind": "ptm", "name": "(Microbial infection) ADP-ribosylthreonine", "position": 66, "source": "UniProtKB" }, { "kind": "ptm", "name": "ADP-ribosylglycine", "position": 76, "source": "UniProtKB" } ], "molecule_id": "P0CG48", "molecule_type": "protein", "name": "Polyubiquitin-C", "organism": { "name": "Homo sapiens", "taxon_id": 9606 }, "provenance": { "deposit_id": "P0CG48", "doi": null, "licence": "CC BY 4.0 (UniProt)", "retrieved": "2026-10-19", "source": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0CG48/entry" }, "sequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGV", "sequence_length": 685 }, "molecule_id": "P0CG48", "states": [ { "assumptions": [], "basis": "observed", "description": "Native globular fold, as in 1UBQ. Ensemble states from NMR dynamics are not yet in the pilot.", "family_label": null, "molecule_id": "P0CG48", "name": "folded (native)", "parent_state": null, "population": null, "provenance": { "deposit_id": null, "doi": null, "licence": "Project licence (pending decision)", "retrieved": "2026-10-19", "source": "Conformome curation (P0CG48.yaml)", "url": "https://github.com/matth55/conformome/blob/HEAD/curation/P0CG48.yaml" }, "representative_model": "Ub-folded-cif", "secondary_structure": null, "state_id": "Ub-folded", "status": "draft" } ], "transitions": [] }