Research workbench
Cryo-EM structure of Csm-crRNA-target RNA ternary complex in type III-A CRISPR-Cas system
Analyse Cryo-EM structure of 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
- 6MUR
- Type
- protein + RNA
- Length
- 2,207 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Thermococcus onnurineus; Thermococcus onnurineus (strain NA1); SYNTHETIC…
- Molecule
- Uncharacterized protein; Uncharacterized protein Csm3; RNA (27-mer); RNA…
- UniProt
- B6YWB8, B6YWB9, B6YWC0, B6YWC1, B6YWC2
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.1 · 8 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 771 | 40% helix, 13% strand | B6YWB8 |
| B | Uncharacterized protein | protein | 162 | 67% helix, 0% strand | B6YWB9 |
| C | Uncharacterized protein Csm3 | protein | 278 | 24% helix, 26% strand | B6YWC0 |
| D | Uncharacterized protein Csm3 | protein | 287 | 22% helix, 26% strand | B6YWC0 |
| E | Uncharacterized protein | protein | 286 | 22% helix, 27% strand | B6YWC1 |
| G | RNA (27-mer) | rna | 27 | — | — |
| H | RNA (5'-R(P*GP*CP*AP*AP*AP*CP*CP*GP*CP*CP*UP*CP*UP*GP*CP*CP*CP*GP*C)-3') | rna | 19 | — | — |
| F | Uncharacterized protein | protein | 377 | 31% helix, 16% strand | B6YWC2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, C, D
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 | 770 | 0.87 | 0.90 | 94 | empty |
| 2 | 226 | 0.83 | 0.96 | 37 | empty |
| 3 | 457 | 0.83 | 0.90 | 60 | empty |
| 4 | 388 | 0.78 | 0.88 | 39 | empty |
| 5 | 88 | 0.76 | 0.98 | 26 | empty |
Interfaces
24 interfaces between chains.
- C–D · 2108 Ų buried · 29 hydrogen bonds · protein-protein
- C–E · 1682 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 1592 Ų buried · 17 hydrogen bonds · protein-protein
- E–G · 1537 Ų buried · 34 hydrogen bonds · protein-nucleic
- D–G · 1362 Ų buried · 29 hydrogen bonds · protein-nucleic
Compared structures
- 6MUR · Cryo-EM structure of csm-crrna-target RNA ternary complex in type III- a CRISPR-CAS system · the same entry in another collection · chain H against H, 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 6MUR · PDBe 6MUR · UniProt B6YWB8 · UniProt B6YWB9 · UniProt B6YWC0 · UniProt B6YWC1 · UniProt B6YWC2
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