Research workbench
Cryo-EM structure of AcrVIA1-Cas13(crRNA) complex
Analyse Cryo-EM structure of AcrVIA1-Cas13(crRNA) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VRB
- Type
- protein + RNA
- Length
- 1,312 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.0
- Source
- Listeria seeligeri; Listeria seeligeri serovar 1/2b (strain ATCC 35967 / DSM…
- Molecule
- RNA (52-mer); CRISPR-associated endoribonuclease Cas13a; AcrVIA1
- EC
- 3.1.-.-
- UniProt
- P0DPB8
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 3.0 · 3 distinct chains · 51% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA (52-mer) | rna | 52 | — | — |
| A | CRISPR-associated endoribonuclease Cas13a (EC 3.1.-.-) | protein | 1031 | 52% helix, 2% strand | P0DPB8 |
| C | AcrVIA1 | protein | 229 | 47% helix, 13% strand | — |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.88 | 0.89 | 116 | empty |
| 2 | 678 | 0.87 | 0.92 | 79 | empty |
| 3 | 165 | 0.80 | 0.96 | 33 | empty |
| 4 | 395 | 0.78 | 0.88 | 34 | empty |
| 5 | 255 | 0.74 | 0.88 | 27 | empty |
Interfaces
3 interfaces between chains.
- B–A · 6337 Ų buried · 121 hydrogen bonds · protein-nucleic
- A–C · 1588 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 554 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 6VRB · Cryo-EM structure of ACRVIA1-CAS13(CRRNA) complex · the same entry in another collection · chain A against A, TM-score 1.00
- P0DPB8 · AlphaFold monomer V2.0 prediction for CRISPR-associated endoribonuclease CAS13A (P0DPB8) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 P0DPB8
- Elsewhere: RCSB PDB 6VRB · PDBe 6VRB · UniProt P0DPB8
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