› 6ozp

X-ray diffraction
1.96Å resolution

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 180 min soak in 10 mM Mn2+

Released:
DOI: 10.2210/pdb6ozp/pdb
PDB entry 6ozp coloured by chain, front view.
PDB entry 6ozp coloured by chain, side view.
PDB entry 6ozp 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 hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113233 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (3 distinct):
Endonuclease V Chains: A, B
Molecule details ›
Chains: A, B
Length: 245 amino acids
Theoretical weight: 27.21 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8C9A2 (Residues: 8-252; Coverage: 73%)
Gene name: Endov
Sequence domains: Endonuclease V
RNA (5'-R(P*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 12 nucleotides
Theoretical weight: 3.77 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA/RNA (5'-R(*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*A)-3') Chains: c, d
Molecule details ›
Chains: c, d
Length: 11 nucleotides
Theoretical weight: 3.47 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand MN 11 x MN
Ligand GOL 2 x GOL
Ligand PG4 2 x PG4
Ligand EDO 6 x EDO
Ligand PGE 3 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 72.031Å b: 73.006Å c: 155.76Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.175 0.201
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

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

1 mention without citation

Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes.
Jones et al. (2022)