Research workbench
Cryo-EM structure of larger Csm-crRNA-target RNA ternary complex in type III-A CRISPR-Cas system
Analyse Cryo-EM structure of larger Csm-crRNA-target RNA ternary complex in type III-A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MUS
- Type
- protein + RNA
- Length
- 2,587 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.6
- Source
- Thermococcus onnurineus; SYNTHETIC CONSTRUCT
- Molecule
- Uncharacterized protein Csm1; Uncharacterized protein Csm2; Uncharacterized protein Csm3…
- UniProt
- B6YWB8, B6YWB9, B6YWC0, B6YWC1, B6YWC2
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 3.6 · 10 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein Csm1 | protein | 772 | 41% helix, 14% strand | B6YWB8 |
| B | Uncharacterized protein Csm2 | protein | 141 | 67% helix, 0% strand | B6YWB9 |
| C | Uncharacterized protein Csm3 | protein | 277 | 19% helix, 25% strand | B6YWC0 |
| D | Uncharacterized protein Csm3 | protein | 287 | 20% helix, 25% strand | B6YWC0 |
| E | Uncharacterized protein Csm4 | protein | 279 | 19% helix, 30% strand | B6YWC1 |
| G | RNA (33-mer) | rna | 33 | — | — |
| H | RNA (25-mer) | rna | 25 | — | — |
| J | Uncharacterized protein Csm2 | protein | 121 | 66% helix, 0% strand | B6YWB9 |
| K | Uncharacterized protein Csm3 | protein | 275 | 22% helix, 22% strand | B6YWC0 |
| F | Uncharacterized protein Csm5 | protein | 377 | 31% helix, 16% strand | B6YWC2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C, D, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.83 | 0.87 | 77 | empty |
| 2 | 900 | 0.83 | 0.85 | 72 | empty |
| 3 | 864 | 0.79 | 0.82 | 79 | empty |
| 4 | 398 | 0.79 | 0.88 | 44 | empty |
| 5 | 423 | 0.76 | 0.85 | 63 | empty |
Interfaces
31 interfaces between chains.
- C–D · 2137 Ų buried · 22 hydrogen bonds · protein-protein
- D–K · 2065 Ų buried · 26 hydrogen bonds · protein-protein
- C–E · 1680 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 1578 Ų buried · 11 hydrogen bonds · protein-protein
- E–G · 1534 Ų buried · 34 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6MUS · Cryo-EM structure of larger csm-crrna-target RNA ternary complex in type III-a CRISPR-CAS… · the same entry in another collection · chain K against K, TM-score 1.00
- B6YWB8 · AlphaFold monomer V2.0 prediction for CRISPR system single-strand- specific… · a predicted model of the same protein · chain A against A, TM-score 0.98
- B6YWC1 · AlphaFold monomer V2.0 prediction for CRISPR system cms protein CSM4 (B6YWC1) · a predicted model of the same protein · chain E against A, TM-score 0.96
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B6YWB8
- Every structure of UniProt B6YWB9
- Every structure of UniProt B6YWC0
- Every structure of UniProt B6YWC1
- Every structure of UniProt B6YWC2
- Elsewhere: RCSB PDB 6MUS · PDBe 6MUS · UniProt B6YWB8 · UniProt B6YWB9 · UniProt B6YWC0 · UniProt B6YWC1 · UniProt B6YWC2
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