› 6o7e

Electron Microscopy
3.2Å resolution

Cryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with AMPPNP in type III-A CRISPR-Cas system

Released:
DOI: 10.2210/pdb6o7e/pdb
PDB entry 6o7e coloured by chain, front view.
PDB entry 6o7e coloured by chain, side view.
PDB entry 6o7e coloured by chain, top view.
Source organism: Thermococcus onnurineus NA1
Primary publication:
Second Messenger cA4 Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path.
Jia N, Jones R, Sukenick G, Patel DJ
Mol Cell 75 933-943.e6 (2019)
PMID: 31326272
Related structures: EMD-0640

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-110422 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (7 distinct):
CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) Chain: A
Molecule details ›
Chain: A
Length: 791 amino acids
Theoretical weight: 89.68 KDa
Source organism: Thermococcus onnurineus NA1
Expression system: Escherichia coli
UniProt:
  • Canonical: B6YWB8 (Residues: 1-777; Coverage: 100%)
Gene names: TON_0893, cas10, csm1
Sequence domains:
CRISPR system Cms protein Csm2 Chain: B
Molecule details ›
Chain: B
Length: 187 amino acids
Theoretical weight: 21.21 KDa
Source organism: Thermococcus onnurineus NA1
Expression system: Escherichia coli
UniProt:
  • Canonical: B6YWB9 (Residues: 1-186; Coverage: 100%)
Gene name: TON_0894
Sequence domains: Csm2 Type III-A
CRISPR system Cms endoribonuclease Csm3 Chains: C, D
Molecule details ›
Chains: C, D
Length: 291 amino acids
Theoretical weight: 32.81 KDa
Source organism: Thermococcus onnurineus NA1
Expression system: Escherichia coli
UniProt:
  • Canonical: B6YWC0 (Residues: 1-290; Coverage: 100%)
Gene name: TON_0895
Sequence domains: RAMP superfamily
CRISPR system Cms protein Csm4 Chain: E
Molecule details ›
Chain: E
Length: 289 amino acids
Theoretical weight: 32.35 KDa
Source organism: Thermococcus onnurineus NA1
Expression system: Escherichia coli
UniProt:
  • Canonical: B6YWC1 (Residues: 1-289; Coverage: 100%)
Gene names: TON_0896, csm4
CRISPR system Cms protein Csm5 Chain: Y
Molecule details ›
Chain: Y
Length: 378 amino acids
Theoretical weight: 40.59 KDa
Source organism: Thermococcus onnurineus NA1
Expression system: Escherichia coli
UniProt:
  • Canonical: B6YWC2 (Residues: 1-397; Coverage: 94%)
Gene name: TON_0897
Sequence domains: RAMP superfamily
RNA (38-MER) Chain: G
Molecule details ›
Chain: G
Length: 38 nucleotides
Theoretical weight: 12.46 KDa
RNA (40-MER) Chain: H
Molecule details ›
Chain: H
Length: 40 nucleotides
Theoretical weight: 12.75 KDa

Ligands and Environments

3 bound ligands:
Ligand ZN 3 x ZN
Ligand ANP 2 x ANP
Ligand MN 3 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-0640
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Structure-based functional mechanisms and biotechnology applications of anti-CRISPR proteins.
Jia et al. (2021)
4 more

2 mentions without citation

Bacterial origins of cyclic nucleotide-activated antiviral immune signaling.
Patel et al. (2022)
1 more