› 5f9r

X-ray diffraction
3.4Å resolution

Crystal structure of catalytically-active Streptococcus pyogenes CRISPR-Cas9 in complex with single-guided RNA and double-stranded DNA primed for target DNA cleavage

Released:
DOI: 10.2210/pdb5f9r/pdb
PDB entry 5f9r coloured by chain, front view.
PDB entry 5f9r coloured by chain, side view.
PDB entry 5f9r coloured by chain, top view.
Source organisms:
Primary publication:
Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage.
Jiang F, Taylor DW, Chen JS, Kornfeld JE, Zhou K, Thompson AJ, Nogales E, Doudna JA
Science 351 867-71 (2016)
PMID: 26841432

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-118667 (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: 158.7 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:
DNA (30-MER) Chain: C
Molecule details ›
Chain: C
Length: 30 nucleotides
Theoretical weight: 9.09 KDa
Source organism: Lambdapapillomavirus 1
Expression system: Not provided
DNA (5'-D(P*AP*TP*GP*AP*GP*AP*CP*GP*CP*TP*GP*GP*AP*GP*TP*AP*CP*AP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 30 nucleotides
Theoretical weight: 9.36 KDa
Source organism: Lambdapapillomavirus 1
Expression system: Not provided
RNA (116-MER) Chain: A
Molecule details ›
Chain: A
Length: 118 nucleotides
Theoretical weight: 38.29 KDa
Source organism: Streptococcus pyogenes MGAS8232
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand SO4 3 x SO4
1 modified residue:
Ligand GTP 1 x GTP

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: F222
Unit cell:
a: 147.94Å b: 230.1Å c: 417.65Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.24 0.237 0.299
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

79 review citations

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

84 mentions without citation

The Revolution Continues: Newly Discovered Systems Expand the CRISPR-Cas Toolkit.
Murugan et al. (2017)
83 more