› 8kak

X-ray diffraction
3.6Å resolution

Crystal structure of SpyCas9 in complex with sgRNA and 18nt target DNA

Released:
DOI: 10.2210/pdb8kak/pdb
PDB entry 8kak coloured by chain, front view.
PDB entry 8kak coloured by chain, side view.
PDB entry 8kak coloured by chain, top view.
Source organism: Streptococcus pyogenes serotype M1
Primary publication:
Trans-nuclease activity of Cas9 activated by DNA or RNA target binding.
Chen J, Chen Y, Huang L, Lin X, Chen H, Xiang W, Liu L
Nat Biotechnol (2024)
PMID: 38811761

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-245009 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (4 distinct):
CRISPR-associated endonuclease Cas9/Csn1 Chains: B, F
Molecule details ›
Chains: B, F
Length: 1368 amino acids
Theoretical weight: 158.59 KDa
Source organism: Streptococcus pyogenes serotype M1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q99ZW2 (Residues: 1-1368; Coverage: 100%)
Gene names: SPy_1046, cas9, csn1
Sequence domains:
DNA (26-MER) Chains: C, G
Molecule details ›
Chains: C, G
Length: 26 nucleotides
Theoretical weight: 7.92 KDa
Source organism: Streptococcus pyogenes serotype M1
Expression system: Not provided
DNA (5'-D(*TP*TP*TP*AP*GP*GP*TP*AP*TP*TP*G)-3') Chains: D, H
Molecule details ›
Chains: D, H
Length: 11 nucleotides
Theoretical weight: 3.39 KDa
Source organism: Streptococcus pyogenes serotype M1
Expression system: Not provided
RNA (98-MER) Chains: A, E
Molecule details ›
Chains: A, E
Length: 98 nucleotides
Theoretical weight: 31.61 KDa
Source organism: Streptococcus pyogenes serotype M1
Expression system: Escherichia coli DH5[alpha]

Ligands and Environments

1 bound ligand:
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P1
Unit cell:
a: 70.742Å b: 104.97Å c: 184.309Å
α: 75.819° β: 78.675° γ: 72.631°
R-values:
R R work R free
0.266 0.265 0.297
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided
  • Escherichia coli DH5[alpha]

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