› 5wn3

X-ray diffraction
2Å resolution

APE1 F266A exonuclease substrate complex with a C/T mismatch

Released:
DOI: 10.2210/pdb5wn3/pdb
PDB entry 5wn3 coloured by chain, front view.
PDB entry 5wn3 coloured by chain, side view.
PDB entry 5wn3 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-119351 (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: 31.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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*(DV3))-3') Chain: D
Molecule details ›
Chain: D
Length: 10 nucleotides
Theoretical weight: 3.08 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chain: E
Molecule details ›
Chain: E
Length: 21 nucleotides
Theoretical weight: 6.42 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand CA 1 x CA
Ligand EDO 4 x EDO
Ligand NA 3 x NA
Ligand CL 2 x CL
1 modified residue:
Ligand C7R 1 x C7R

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P21
Unit cell:
a: 71.144Å b: 65.545Å c: 91.441Å
α: 90° β: 110.08° γ: 90°
R-values:
R R work R free
0.211 0.21 0.258
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

10 review citations

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

1 mention without citation

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