Research workbench
Cryo-EM structure of csm-crrna-target RNA ternary bigger complex in complex with CA4 in type III-a CRISPR-CAS system
Analyse Cryo-EM structure of csm-crrna-target RNA ternary bigger complex in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O7I
- Type
- protein + RNA
- Length
- 2,519 residues
- Chains
- 11
- 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
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 11 distinct chains · 31% helix, 18% 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 | 741 | 40% helix, 13% strand | B6YWB8 |
| B | CSM2 | protein | 146 | 45% helix, 0% strand | B6YWB9 |
| C | CSM3 | protein | 275 | 20% helix, 25% strand | B6YWC0 |
| D | CSM3 | protein | 272 | 22% helix, 25% strand | B6YWC0 |
| E | CSM4 | protein | 279 | 22% helix, 32% strand | B6YWC1 |
| J | CSM2 | protein | 121 | 52% helix, 0% strand | B6YWB9 |
| G | RNA (38-mer) | rna | 26 | — | — |
| H | RNA (40-mer) | rna | 19 | — | — |
| K | CSM3 | protein | 275 | 21% helix, 23% strand | B6YWC0 |
| I | RNA (5'-R(P*AP*AP*AP*A)-3') | rna | 4 | — | — |
| F | CSM5 | protein | 361 | 28% helix, 15% strand | — |
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 | 737 | 0.82 | 0.86 | 73 | empty |
| 2 | 1100 | 0.81 | 0.82 | 97 | empty |
| 3 | 904 | 0.80 | 0.82 | 75 | empty |
| 4 | 121 | 0.77 | 0.96 | 22 | empty |
| 5 | 97 | 0.76 | 0.97 | 31 | empty |
Interfaces
32 interfaces between chains.
- C–D · 2047 Ų buried · 24 hydrogen bonds · protein-protein
- D–K · 2036 Ų buried · 21 hydrogen bonds · protein-protein
- C–E · 1720 Ų buried · 23 hydrogen bonds · protein-protein
- E–G · 1519 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–E · 1392 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6O7I · Cryo-EM structure of Csm-crRNA-target RNA ternary bigger complex in complex with cA4 in… · the same entry in another collection · chain F against F, 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 0.99
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 6O7I · PDBe 6O7I · UniProt B6YWB8 · UniProt B6YWB9 · UniProt B6YWC0 · UniProt B6YWC1
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