› 6cvo

X-ray diffraction
2.4Å resolution

Human Aprataxin (Aptx) bound to nicked RNA-DNA, AMP and Zn product complex

Released:
DOI: 10.2210/pdb6cvo/pdb
PDB entry 6cvo coloured by chain, front view.
PDB entry 6cvo coloured by chain, side view.
PDB entry 6cvo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease.
Tumbale P, Schellenberg MJ, Mueller GA, Fairweather E, Watson M, Little JN, Krahn J, Waddell I, London RE, Williams RS
EMBO J 37 (2018)
PMID: 29934293

Function and Biology Details

Reactions catalysed: 
Adenosine-5'-diphospho-5'-(DNA) + H(2)O = AMP + phospho-5'-(DNA)
(DNA)-3'-diphospho-5'-guanosine + H(2)O = (DNA)-3'-phosphate + GMP
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113209 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (3 distinct):
Aprataxin Chains: A, B
Molecule details ›
Chains: A, B
Length: 182 amino acids
Theoretical weight: 21.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7Z2E3 (Residues: 179-356; Coverage: 50%)
Gene names: APTX, AXA1
Sequence domains:
Structure domains: HIT-like
DNA (5'-D(*AP*AP*CP*AP*GP*C)-3') Chains: E, H
Molecule details ›
Chains: E, H
Length: 6 nucleotides
Theoretical weight: 1.8 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA/RNA (5'-R(P*G)-D(P*TP*TP*CP*TP*AP*TP*AP*TP*AP*TP*AP*GP*AP*AP*CP*GP*CP*TP*GP*TP*T)-3') Chains: D, G
Molecule details ›
Chains: D, G
Length: 22 nucleotides
Theoretical weight: 6.77 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand AMP 2 x AMP
Ligand ZN 2 x ZN
Ligand BME 2 x BME
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 58.913Å b: 72.547Å c: 147.164Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.184 0.222
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Molecular and physiological consequences of faulty eukaryotic ribonucleotide excision repair.
Kellner et al. (2020)
6 other articles

2 mentions without citation

Known Cellular and Receptor Interactions of Animal and Human Coronaviruses: A Review.
Everest et al. (2022)
1 more