A-riboswitch from Vibrio vulnificus (PDB 1Y26, chain X)
RNAcentral URS000080DF85_672 · Rfam RF00167 · Vibrio vulnificus · 71 nt
13evidence items
10mapped to a state
3states
2techniques
2sources
0conflicts
Coverage grid
Mapped evidence per state and technique. Shaded rows rest on a single technique. Badge = best data level in the cell: raw (traces, images, FIDs: can be re-analysed), proc (maps, curves, tables, trajectories) or rep (values in the paper only).
| State | Basis | xray | rfam_covariation | Total |
|---|---|---|---|---|
| ligand-free aptamer ADD-apo | observed (one method) | proc 1 | · | 1 |
| ligand-bound intermediate ADD-intermediate | observed (one method) | proc 1 | · | 1 |
| adenine-bound aptamer ADD-bound | observed (one method) | proc 8 | · | 8 |
Unmapped evidence: 3 of 13 items. Mappings come from curator assignments and curated rules; see About for how rules work.
Sources
| Source | Evidence | Mapped |
|---|---|---|
| NAKB | 12 | 10 |
| Rfam | 1 | 0 |
Curated rules applied
add-adenine-bound: 3 items
Structure
Choose a state. Each model is badged observed or inferred; assumptions are one click away.
States and transitions
| State | Basis | Parent | Description |
|---|---|---|---|
| ligand-free aptamer ADD-apo | observed | — | Aptamer without adenine, as in 5E54 (room-temperature XFEL structure; two conformers in the asymmetric unit, apo1 and apo2, which differ in the length of P1). The 5E54 construct has a different P1 sequence from this page's sequence, so no pairing is given here. Family vocabulary riboswitch: aptamer: aptamer_unbound |
| ligand-bound intermediate ADD-intermediate | observed | — | Adenine bound to an aptamer that has not yet reached the fully bound fold, trapped by mix-and-inject serial crystallography, as in 5SWD. Same construct as 5E54. |
| adenine-bound aptamer ADD-bound | observed | — | Aptamer folded around adenine, as in 1Y26 (2.1 Å, Mg2+): P1, P2 and P3 around a three-way junction, the L2-L3 kissing loop (G37-C61, G38-C60; brackets [ ]), the U22-A52 pair of the binding pocket (brackets { }) and adenine paired with U74. Family vocabulary riboswitch: aptamer: aptamer_bound ((((((((({..((((((......[[.))))))(.....})((((((]].....))))))..)))))))))Pairing from 1Y26, canonical cWW pairs from FR3D (BGSU RNA 3D Hub), author numbering 13-83 = positions 1-71 |
No transitions recorded in this version (no rate or free-energy evidence has been curated yet).
Evidence
One row per deposit or experiment. Filter by technique, environment or text. Unmapped evidence is listed too.
| Evidence | Technique | Observable | Conditions | Mapped to state |
|---|---|---|---|---|
| EV-NAKB-1Y26-1 NAKB | xray | resolution: 2.1 Å | in vitro · ligands ADE A-riboswitch-adenine complex · Vibrio vulnificus A-riboswitch (chains X); same sequence | adenine-bound aptamer · curator:draft (unreviewed) · high Adenine (ADE) bound, this exact sequence; anchor structure. |
| EV-NAKB-4LX5-1 NAKB | xray | resolution: 2.13 Å | in vitro · ligands 29G X-ray crystal structure of the M6" riboswitch aptamer bound to pyrimido[4,5-d]pyrimidine-2,4-diamine (PPDA) · Mutated adenine riboswitch aptamer (chains A); other construct of the same Rfam family (RF00167) and organism, 71 nt | adenine-bound aptamer · curator:draft (unreviewed) · low Engineered M6'' aptamer bound to a synthetic ligand (PPDA) instead of adenine; bound fold assumed similar. |
| EV-NAKB-4LX6-1 NAKB | xray | resolution: 2.15 Å | in vitro · ligands 29H X-ray crystal structure of the M6C" riboswitch aptamer bound to 2-aminopyrimido[4,5-d]pyrimidin-4(3H)-one (PPAO) · Mutated adenine riboswitch aptamer (chains A); other construct of the same Rfam family (RF00167) and organism, 71 nt | adenine-bound aptamer · curator:draft (unreviewed) · low Engineered M6C'' aptamer bound to a synthetic ligand (PPAO) instead of adenine; bound fold assumed similar. |
| EV-NAKB-4TZX-1 NAKB | xray | resolution: 2.01 Å | in vitro · ligands ADE Vibrio Vulnificus Adenine Riboswitch variant, grown in Mg2+ · Vibrio vulnificus Adenine Riboswitch (chains X); other construct of the same Rfam family (RF00167) and organism, 71 nt | adenine-bound aptamer · rule:add-adenine-bound · medium Structure with adenine modelled and not titled as an intermediate or transitional state; adenine-bound aptamer structures share the bound fold. |
| EV-NAKB-4TZY-1 NAKB | xray | resolution: 2.57 Å | in vitro · ligands ADE Vibrio vulnificus Adenine Riboswitch Variant, grown in both Sr2+ and Mg2+ · Vibrio vulnificus Adenine Riboswitch (chains X); other construct of the same Rfam family (RF00167) and organism, 71 nt | adenine-bound aptamer · rule:add-adenine-bound · medium Structure with adenine modelled and not titled as an intermediate or transitional state; adenine-bound aptamer structures share the bound fold. |
| EV-NAKB-4XNR-1 NAKB | xray | resolution: 2.21 Å | in vitro · ligands ADE Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized by Position-selective Labeling of RNA (PLOR), in Complex with Adenine · Vibrio Vulnificus Adenine Riboswitch (chains X); other construct of the same Rfam family (RF00167) and organism, 71 nt | adenine-bound aptamer · curator:draft (unreviewed) · high Title: aptamer domain in complex with adenine (PLOR-synthesised). |
| EV-NAKB-5E54-1 NAKB | xray | resolution: 2.3 Å | in vitro Two apo structures of the adenine riboswitch aptamer domain determined using an X-ray free electron laser · Vibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain (chains A,B); other construct of the same Rfam family (RF00167) and organism, 71 nt | ligand-free aptamer · curator:draft (unreviewed) · high Title: two apo structures of the aptamer domain; no adenine modelled. |
| EV-NAKB-5SWD-1 NAKB | xray | resolution: 2.5 Å | in vitro · ligands ADE Structure of the adenine riboswitch aptamer domain in an intermediate-bound state · Vibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain (chains A,B); other construct of the same Rfam family (RF00167) and organism, 71 nt | ligand-bound intermediate · curator:draft (unreviewed) · high Title: aptamer domain in an intermediate-bound state. |
| EV-NAKB-5SWE-1 NAKB | xray | resolution: 3 Å | in vitro · ligands ADE Ligand-bound structure of adenine riboswitch aptamer domain converted in crystal from its ligand-free state using ligand mixing serial femtosecond crystallography · Vibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain (chains X); other construct of the same Rfam family (RF00167) and organism, 71 nt | adenine-bound aptamer · curator:draft (unreviewed) · high Title: ligand-bound structure converted in crystal from the ligand-free state. |
| EV-NAKB-5UZA-1 NAKB | xray | resolution: 2.22 Å | in vitro · ligands ADE Adenine riboswitch aptamer domain labelled with iodo-uridine by position-selective labelling of RNA (PLOR) · RNA (71-MER) (chains X); other construct of the same Rfam family (RF00167) and organism, 71 nt | adenine-bound aptamer · rule:add-adenine-bound · medium Structure with adenine modelled and not titled as an intermediate or transitional state; adenine-bound aptamer structures share the bound fold. |
| EV-NAKB-6VWT-1 NAKB | xray | resolution: 3.03 Å | in vitro · ligands ADE Transitional unit cell 1 of adenine riboswitch aptamer crystal phase transition upon ligand binding · adenine riboswitch aptamer variant (chains A,B); other construct of the same Rfam family (RF00167) and organism, 71 nt | unmapped |
| EV-NAKB-6VWV-1 NAKB | xray | resolution: 3 Å | in vitro · ligands ADE Transitional unit cell 2 of adenine riboswitch aptamer crystal phase transition upon ligand binding · adenine riboswitch aptamer variant (chains A,B); other construct of the same Rfam family (RF00167) and organism, 71 nt | unmapped |
| EV-RFAM-RF00167-2-69 Rfam | rfam_covariation | family_coverage: 0.944 fraction | in silico Rfam RF00167 (Purine): Purine riboswitch aptamer · positions 2-69 of 71 match the family covariance model; type Cis-reg; riboswitch;; consensus structure source: Published; PMID:12787499 | unmapped |
Conflicts
No conflicts found among comparable evidence.
13 evidence items could not be compared: they lack a comparable observable type, a value, or an uncertainty. Absence of a conflict here is not agreement.
Downloads
- Protein bundle (JSON)
- ADD-apo-cif (mmCIF, observed)
- ADD-apo-pdb (PDB, observed)
- ADD-intermediate-cif (mmCIF, observed)
- ADD-intermediate-pdb (PDB, observed)
- ADD-bound-cif (mmCIF, observed)
- ADD-bound-pdb (PDB, observed)
- Curation file (YAML)