Research workbench
Cryo-EM structure of ternary csm-crrna-target RNA with anti-tag sequence complex in type III-a CRISPR-CAS system
Analyse Cryo-EM structure of ternary csm-crrna-target RNA with anti-tag sequence… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MUT
- Type
- protein + RNA
- Length
- 2,154 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 8 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein CSM1 | protein | 747 | 39% helix, 13% strand | B6YWB8 |
| B | Uncharacterized protein CSM2 | protein | 162 | 51% helix, 0% strand | B6YWB9 |
| C | Uncharacterized protein CSM3 | protein | 276 | 20% helix, 26% strand | B6YWC0 |
| D | Uncharacterized protein CSM3 | protein | 267 | 21% helix, 21% strand | B6YWC0 |
| E | Uncharacterized protein CSM4 | protein | 286 | 23% helix, 33% strand | B6YWC1 |
| G | RNA (5'- R(*GP*UP*GP*GP*AP*AP*AP*GP*GP*CP*GP*GP*GP*CP*AP*GP*AP*GP*GP*C)-3') | rna | 20 | — | — |
| H | RNA (5'- R(P*CP*CP*UP*CP*UP*GP*CP*CP*CP*GP*CP*CP*UP*UP*UP*CP*CP*AP*C)-3') | rna | 19 | — | — |
| F | Uncharacterized protein CSM5 | 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 | 1147 | 0.83 | 0.85 | 111 | empty |
| 2 | 471 | 0.80 | 0.87 | 50 | empty |
| 3 | 130 | 0.78 | 0.96 | 20 | empty |
| 4 | 532 | 0.76 | 0.83 | 55 | empty |
| 5 | 303 | 0.76 | 0.88 | 38 | empty |
Interfaces
24 interfaces between chains.
- C–D · 2246 Ų buried · 35 hydrogen bonds · protein-protein
- C–E · 1748 Ų buried · 20 hydrogen bonds · protein-protein
- E–G · 1516 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–E · 1466 Ų buried · 15 hydrogen bonds · protein-protein
- C–G · 1321 Ų buried · 34 hydrogen bonds · protein-nucleic
Compared structures
- 6MUT · Cryo-EM structure of ternary Csm-crRNA-target RNA with anti-tag sequence complex in type… · 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 0.98
- 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 6MUT · PDBe 6MUT · UniProt B6YWB8 · UniProt B6YWB9 · UniProt B6YWC0 · UniProt B6YWC1 · UniProt B6YWC2
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