MolNFT v1 · #158884 · protein + RNA
Cryo-EM structure of csm-crrna-target RNA ternary complex in complex with CA4 in type III-a CRISPR-CAS system
6O7H · CRISPR system single-strand-specific deoxyribonuclease…: “Cryo-EM structure of csm-crrna-target RNA ternary complex in complex with CA4 in type III-a CRISPR-CAS system”. Electron microscopy, 2 ligands (G, ZN), 20 pockets (best…
- PDB
- 6O7H
- Type
- protein + RNA
- Length
- 2,181 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR system single-strand-specific deoxyribonuclease CAS10/CSM1 (subtype III-a); CSM2…
- EC
- 3.1.-.-, 2.7.7.-
- UniProt
- B6YWB8, B6YWB9, B6YWC0, B6YWC1
- Ligands
- G, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 9 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR system single-strand-specific deoxyribonuclease CAS10/CSM1 (subtype III-a) (EC 3.1.-.-, 2.7.7.-) | protein | 771 | 42% helix, 15% strand | B6YWB8 |
| B | CSM2 | protein | 150 | 61% helix, 0% strand | B6YWB9 |
| C | CSM3 | protein | 278 | 24% helix, 25% strand | B6YWC0 |
| D | CSM3 | protein | 285 | 23% helix, 25% strand | B6YWC0 |
| E | CSM4 | protein | 286 | 24% helix, 31% strand | B6YWC1 |
| G | RNA (38-mer) | rna | 27 | — | — |
| H | RNA (40-mer) | rna | 19 | — | — |
| F | CSM5 | protein | 361 | 29% helix, 18% strand | — |
| K | Cyclic DNA CA4 | rna | 4 | — | — |
Ligands and binding sites
- G · Guanosine-5'-monophosphate · ligand · chains A, C, E, H
- 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.84 | 0.95 | 43 | empty |
| 2 | 1139 | 0.81 | 0.83 | 97 | empty |
| 3 | 433 | 0.79 | 0.88 | 57 | empty |
| 4 | 393 | 0.76 | 0.86 | 57 | empty |
| 5 | 336 | 0.76 | 0.87 | 37 | empty |
Interfaces
26 interfaces between chains.
- C–D · 2118 Ų buried · 31 hydrogen bonds · protein-protein
- C–E · 1672 Ų buried · 24 hydrogen bonds · protein-protein
- E–G · 1513 Ų buried · 33 hydrogen bonds · protein-nucleic
- D–G · 1378 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–E · 1360 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6O7H · Cryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with cA4 in type… · 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
- Elsewhere: RCSB PDB 6O7H · PDBe 6O7H · UniProt B6YWB8 · UniProt B6YWB9 · UniProt B6YWC0 · UniProt B6YWC1
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