› 5wn0

X-ray diffraction
2.6Å resolution

APE1 exonuclease substrate complex with a C/G match

Released:
DOI: 10.2210/pdb5wn0/pdb
PDB entry 5wn0 coloured by chain, front view.
PDB entry 5wn0 coloured by chain, side view.
PDB entry 5wn0 coloured by chain, top view.
Source organisms:
Primary publication:
Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.
Whitaker AM, Flynn TS, Freudenthal BD
Nat Commun 9 399 (2018)
PMID: 29374164

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero tetramer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-119348 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA repair nuclease/redox regulator APEX1, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 276 amino acids
Theoretical weight: 31.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P27695 (Residues: 43-318; Coverage: 87%)
Gene names: APE, APE1, APEX, APEX1, APX, HAP1, REF1
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.33 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 10 nucleotides
Theoretical weight: 3.06 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chain: E
Molecule details ›
Chain: E
Length: 21 nucleotides
Theoretical weight: 6.45 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P1
Unit cell:
a: 44.264Å b: 61.942Å c: 73.765Å
α: 82.59° β: 76.88° γ: 85.89°
R-values:
R R work R free
0.222 0.217 0.275
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 review citations

Eukaryotic Base Excision Repair: New Approaches Shine Light on Mechanism.
Beard et al. (2019)
9 more

4 mentions without citation

Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.
Whitaker et al. (2018)
3 more