› 6joo

X-ray diffraction
2.9Å resolution

Crystal structure of Corynebacterium diphtheriae Cas9 in complex with sgRNA and target DNA

Released:
DOI: 10.2210/pdb6joo/pdb
PDB entry 6joo coloured by chain, front view.
PDB entry 6joo coloured by chain, side view.
PDB entry 6joo coloured by chain, top view.
Source organism: Corynebacterium diphtheriae
Primary publication:
Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9.
Hirano S, Abudayyeh OO, Gootenberg JS, Horii T, Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O
Nat Commun 10 1968 (2019)
PMID: 31036811

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120089 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (4 distinct):
CRISPR-associated endonuclease Cas9 Chain: A
Molecule details ›
Chain: A
Length: 927 amino acids
Theoretical weight: 103.97 KDa
Source organism: Corynebacterium diphtheriae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6NKI3 (Residues: 1-497, 664-1084; Coverage: 85%)
Gene names: DIP0036, cas9
Sequence domains:
Non-Target DNA Chain: D
Molecule details ›
Chain: D
Length: 8 nucleotides
Theoretical weight: 2.51 KDa
Target DNA Chain: C
Molecule details ›
Chain: C
Length: 28 nucleotides
Theoretical weight: 8.43 KDa
Guide RNA Chain: B
Molecule details ›
Chain: B
Length: 113 nucleotides
Theoretical weight: 36.32 KDa

Ligands and Environments

2 bound ligands:
Ligand EDO 2 x EDO
Ligand ZN 1 x ZN
1 modified residue:
Ligand MSE 15 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: C2
Unit cell:
a: 139.015Å b: 118.999Å c: 116.272Å
α: 90° β: 113.59° γ: 90°
R-values:
R R work R free
0.222 0.221 0.254
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Harnessing the potential of CRISPR-based platforms to advance the field of hospital medicine.
McCarthy MW. (2020)
5 more

2 mentions without citation

Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering.
Esquerra-Ruvira et al. (2023)
1 more