› 7qqo

X-ray diffraction
3Å resolution

SpCas9 bound to AAVS1 off-target1 DNA substrate

Released:
DOI: 10.2210/pdb7qqo/pdb
Model geometry
Fit model/data
PDB entry 7qqo coloured by chain, front view.
PDB entry 7qqo coloured by chain, side view.
PDB entry 7qqo coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for Cas9 off-target activity.
Pacesa M, Lin CH, Cléry A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M
Cell 185 4067-4081.e21 (2022)
PMID: 36306733

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-121859 (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: 1368 amino acids
Theoretical weight: 158.59 KDa
Source organism: Streptococcus pyogenes
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q99ZW2 (Residues: 1-1368; Coverage: 100%)
Gene names: SPy_1046, cas9, csn1
Sequence domains:
AAVS1 off-target1 target strand Chain: C
Molecule details ›
Chain: C
Length: 28 nucleotides
Theoretical weight: 8.44 KDa
Source organism: synthetic construct
Expression system: Not provided
AAVS1 off-target1 non-target strand Chain: D
AAVS1 sgRNA Chain: A

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand K 12 x K
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X06SA
Spacegroup: C2
Unit cell:
a: 178.067Å b: 67.668Å c: 188.44Å
α: 90° β: 111.415° γ: 90°
R-values:
R R work R free
0.214 0.212 0.247
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided
  • synthetic construct

Quick links

Citations

13 review citations

Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing.
Tao et al. (2023)
12 more

1 mention without citation

Structural basis for Cas9 off-target activity.
Pacesa et al. (2022)