› 5b2r

X-ray diffraction
2Å resolution

Crystal structure of the Streptococcus pyogenes Cas9 VQR variant in complex with sgRNA and target DNA (TGA PAM)

Released:
DOI: 10.2210/pdb5b2r/pdb
PDB entry 5b2r coloured by chain, front view.
PDB entry 5b2r coloured by chain, side view.
PDB entry 5b2r coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9.
Hirano S, Nishimasu H, Ishitani R, Nureki O
Mol Cell 61 886-94 (2016)
PMID: 26990991

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118417 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (4 distinct):
CRISPR-associated endonuclease Cas9/Csn1 Chain: B
Molecule details ›
Chain: B
Length: 1372 amino acids
Theoretical weight: 158.98 KDa
Source organism: Streptococcus pyogenes serotype M1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99ZW2 (Residues: 1-1368; Coverage: 100%)
Gene names: SPy_1046, cas9, csn1
Sequence domains:
Target DNA Chain: C
Molecule details ›
Chain: C
Length: 28 nucleotides
Theoretical weight: 8.45 KDa
Source organism: Streptococcus pyogenes
Expression system: Not provided
Non-target DNA, DNA (5'-D(*TP*GP*AP*GP*AP*TP*TP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 8 nucleotides
Theoretical weight: 2.48 KDa
Source organism: Streptococcus pyogenes
Expression system: Not provided
Guide RNA Chain: A
Molecule details ›
Chain: A
Length: 81 nucleotides
Theoretical weight: 26.21 KDa
Source organism: Streptococcus pyogenes
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand K 11 x K
Ligand MG 3 x MG
Ligand EDO 4 x EDO
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: C2
Unit cell:
a: 177.764Å b: 67.744Å c: 187.594Å
α: 90° β: 111.23° γ: 90°
R-values:
R R work R free
0.202 0.2 0.23
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

27 review citations

Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors.
Anzalone et al. (2020)
26 more

7 mentions without citation

CRISPR RNA-guided autonomous delivery of Cas9.
Wilkinson et al. (2019)
6 more