› 5xut

X-ray diffraction
2.4Å resolution

Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and target DNA (TCTA PAM)

Released:
DOI: 10.2210/pdb5xut/pdb
PDB entry 5xut coloured by chain, front view.
PDB entry 5xut coloured by chain, side view.
PDB entry 5xut coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1.
Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu H, Nureki O
Mol Cell 67 633-645.e3 (2017)
PMID: 28781234

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-103174 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (4 distinct):
Cpf1 Chain: A
Molecule details ›
Chain: A
Length: 1231 amino acids
Theoretical weight: 144.17 KDa
Source organism: Lachnospiraceae bacterium ND2006
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A182DWE3 (Residues: 3-1228; Coverage: 100%)
Sequence domains:
DNA (29-MER) Chain: C
Molecule details ›
Chain: C
Length: 29 nucleotides
Theoretical weight: 8.89 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*GP*TP*CP*CP*TP*CP*TP*A)-3') Chain: D
Molecule details ›
Chain: D
Length: 9 nucleotides
Theoretical weight: 2.67 KDa
Source organism: synthetic construct
Expression system: Not provided
crRNA Chain: B
Molecule details ›
Chain: B
Length: 40 nucleotides
Theoretical weight: 12.88 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P41212
Unit cell:
a: 102.45Å b: 102.45Å c: 373.885Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.193 0.238
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

23 review citations

Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing.
Swarts et al. (2018)
22 more

2 mentions without citation

CasX enzymes comprise a distinct family of RNA-guided genome editors.
Liu et al. (2019)
1 more