› 1de9

X-ray diffraction
3Å resolution

HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION

Released:
DOI: 10.2210/pdb1de9/pdb
PDB entry 1de9 coloured by chain, front view.
PDB entry 1de9 coloured by chain, side view.
PDB entry 1de9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected].
Mol CD, Izumi T, Mitra S, Tainer JA
Nature 403 451-6 (2000)
PMID: 10667800

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 domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113675 (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: 31.2 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
5'-d(*CP*TP*AP*C)-3' Chains: U, X
Molecule details ›
Chains: U, X
Length: 4 nucleotides
Theoretical weight: 1.15 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-d(P*(3DR)P*GP*AP*TP*C)-3' Chains: V, Y
Molecule details ›
Chains: V, Y
Length: 5 nucleotides
Theoretical weight: 1.37 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3' Chains: W, Z
Molecule details ›
Chains: W, Z
Length: 9 nucleotides
Theoretical weight: 2.8 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-1
Spacegroup: P212121
Unit cell:
a: 90.06Å b: 98.35Å c: 101.05Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.183 0.274
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

93 review citations

Base excision repair.
Krokan et al. (2013)
92 more

17 mentions without citation

Recognition and repair of chemically heterogeneous structures at DNA ends.
Andres et al. (2015)
16 more