› 5gkp

X-ray diffraction
2.3Å resolution

Crystal structure of the EndoG worm homologue CPS-6 H148A/F122A in complex with DNA

Released:
DOI: 10.2210/pdb5gkp/pdb
Model geometry
Fit model/data
PDB entry 5gkp coloured by chain, front view.
PDB entry 5gkp coloured by chain, side view.
PDB entry 5gkp coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer.
Lin JL, Wu CC, Yang WZ, Yuan HS
OpenAccess logo Nucleic Acids Res 44 10480-10490 (2016)
PMID: 27738134

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-118706 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Endonuclease G, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 252 amino acids
Theoretical weight: 28.7 KDa
Source organism: Caenorhabditis elegans
Expression system: Escherichia coli
UniProt:
  • Canonical: Q95NM6 (Residues: 63-305; Coverage: 79%)
Gene names: C41D11.8, cps-6
Sequence domains: DNA/RNA non-specific endonuclease
Structure domains: Extracellular Endonuclease, subunit A
DNA (5'-D(*TP*TP*TP*TP*T)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 8 nucleotides
Theoretical weight: 2.41 KDa
Source organism: unidentified
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: NSRRC BEAMLINE BL15A1
Spacegroup: P212121
Unit cell:
a: 56.672Å b: 72.562Å c: 127.914Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.174 0.252
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 citation in other articles

Selective mitochondrial DNA degradation following double-strand breaks.
Moretton et al. (2017)
6 more

3 mentions without citation

Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer.
Lin et al. (2016)
2 more