› 5b43

X-ray diffraction
2.8Å resolution

Crystal structure of Acidaminococcus sp. Cpf1 in complex with crRNA and target DNA

Released:
DOI: 10.2210/pdb5b43/pdb
PDB entry 5b43 coloured by chain, front view.
PDB entry 5b43 coloured by chain, side view.
PDB entry 5b43 coloured by chain, top view.
Source organisms:
Primary publication:
Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA.
Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O
Cell 165 949-62 (2016)
PMID: 27114038

Function and Biology Details

Reactions catalysed: 
Endonucleolytic cleavage to 5'-phosphodinucleotide and 5'-phosphooligonucleotide end-products
RNA = a 5'-hydroxy-ribonucleotide + n nucleoside-2',3'-cyclophosphates
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-118424 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (4 distinct):
CRISPR-associated endonuclease Cas12a Chain: A
Molecule details ›
Chain: A
Length: 1310 amino acids
Theoretical weight: 151.7 KDa
Source organism: Acidaminococcus sp. BV3L6
Expression system: Escherichia coli
UniProt:
  • Canonical: U2UMQ6 (Residues: 1-1307; Coverage: 100%)
Gene names: HMPREF1246_0236, cas12a, cpf1
Sequence domains:
DNA (34-MER) Chain: C
Molecule details ›
Chain: C
Length: 34 nucleotides
Theoretical weight: 10.44 KDa
Source organism: Acidaminococcus
Expression system: Not provided
DNA (5'-D(*CP*AP*GP*TP*CP*CP*TP*TP*TP*A)-3') Chain: D
Molecule details ›
Chain: D
Length: 10 nucleotides
Theoretical weight: 2.99 KDa
Source organism: Acidaminococcus
Expression system: Not provided
RNA (43-MER) Chain: B
Molecule details ›
Chain: B
Length: 43 nucleotides
Theoretical weight: 13.76 KDa
Source organism: Acidaminococcus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand EDO 3 x EDO
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 81.515Å b: 136.732Å c: 196.909Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.22 0.257
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

104 review citations

The CRISPR tool kit for genome editing and beyond.
Adli M. (2018)
103 more

32 mentions without citation

CRISPR-Mediated Epigenome Editing.
Enríquez P. (2016)
31 more