› 6ozi

X-ray diffraction
2.3Å resolution

Crystal structure of Ciona intestinalis (Ci) Endonuclease V (D234N) in complex with a 23mer DNA containing an inosine followed by a ribo-adenosine

Released:
DOI: 10.2210/pdb6ozi/pdb
Model geometry
Fit model/data
PDB entry 6ozi coloured by chain, front view.
PDB entry 6ozi coloured by chain, side view.
PDB entry 6ozi coloured by chain, top view.
Source organisms:
Primary publication:
Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Wu J, Samara NL, Kuraoka I, Yang W
Mol Cell 76 44-56.e3 (2019)
PMID: 31444105

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-113226 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (2 distinct):
endonuclease V isoform X2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 244 amino acids
Theoretical weight: 27.61 KDa
Source organism: Ciona intestinalis
Expression system: Escherichia coli
DNA/RNA (23-MER) Chains: C, D
Molecule details ›
Chains: C, D
Length: 23 nucleotides
Theoretical weight: 7.03 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand K 4 x K
Ligand PGE 2 x PGE
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU MICROMAX-007 HF
Unit cell:
a: 51.079Å b: 81.428Å c: 166.034Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.174 0.201
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Function and Molecular Mechanism of the DNA Damage Response in Immunity and Cancer Immunotherapy.
Ye et al. (2021)
5 more

1 mention without citation

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Wu et al. (2019)