Research workbench
Cryo-EM structure of csm-crrna-target RNA ternary complex in complex with amppnp in type III-a CRISPR-CAS system
Analyse Cryo-EM structure of csm-crrna-target RNA ternary complex in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O7E
- Type
- protein + RNA
- Length
- 2,185 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CSM1; CSM2; CSM3; CSM4; RNA (38-mer); RNA (40-mer); CSM5
- EC
- 3.1.-.-, 2.7.7.-
- UniProt
- B6YWB8, B6YWB9, B6YWC0, B6YWC1
- Ligands
- ANP, ZN, MN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CSM1 (EC 3.1.-.-, 2.7.7.-) | protein | 771 | 39% helix, 14% strand | B6YWB8 |
| B | CSM2 | protein | 159 | 62% helix, 0% strand | B6YWB9 |
| C | CSM3 | protein | 278 | 22% helix, 22% strand | B6YWC0 |
| D | CSM3 | protein | 284 | 22% helix, 22% strand | B6YWC0 |
| E | CSM4 | protein | 286 | 23% helix, 30% strand | B6YWC1 |
| G | RNA (38-mer) | rna | 27 | — | — |
| H | RNA (40-mer) | rna | 19 | — | — |
| Y | CSM5 | protein | 361 | 22% helix, 15% strand | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, E
- ZN · Zinc ion · metal · 3 copies · chains A, C, D
- MN · Manganese (II) ion · metal · 3 copies · chains A
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 | 641 | 0.84 | 0.89 | 69 | empty |
| 2 | 411 | 0.82 | 0.90 | 45 | empty |
| 3 | 999 | 0.82 | 0.83 | 96 | empty |
| 4 | 445 | 0.78 | 0.86 | 46 | empty |
| 5 | 125 | 0.77 | 0.96 | 20 | empty |
Interfaces
24 interfaces between chains.
- C–D · 2100 Ų buried · 26 hydrogen bonds · protein-protein
- C–E · 1683 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 1610 Ų buried · 19 hydrogen bonds · protein-protein
- E–G · 1514 Ų buried · 35 hydrogen bonds · protein-nucleic
- D–G · 1376 Ų buried · 30 hydrogen bonds · protein-nucleic
Compared structures
- 6O7E · Cryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with AMPPNP in type… · the same entry in another collection · chain Y against Y, 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 6O7E · PDBe 6O7E · UniProt B6YWB8 · UniProt B6YWB9 · UniProt B6YWC0 · UniProt B6YWC1
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