› 4ndf

X-ray diffraction
1.94Å resolution

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

Released:
DOI: 10.2210/pdb4ndf/pdb
PDB entry 4ndf coloured by chain, front view.
PDB entry 4ndf coloured by chain, side view.
PDB entry 4ndf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity.
Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA, Williams RS
OpenAccess logo Nature 506 111-5 (2014)
PMID: 24362567

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-505796 (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 BL21(DE3)
UniProt:
  • Canonical: Q7Z2E3 (Residues: 179-356; Coverage: 50%)
  • Best match: Q7Z2E3-2 (Residues: 1-168)
Gene names: APTX, AXA1
Sequence domains:
Structure domains: HIT-like
5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3' Chains: E, H
Molecule details ›
Chains: E, H
Length: 10 nucleotides
Theoretical weight: 3.04 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3' Chains: D, G
Molecule details ›
Chains: D, G
Length: 10 nucleotides
Theoretical weight: 3.07 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand AMP 2 x AMP
Ligand ZN 2 x ZN
Ligand NA 1 x NA
Ligand BME 2 x BME
Ligand K 1 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 40.429Å b: 116.211Å c: 117.141Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.171 0.205
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

22 review citations

DNA replication stress: causes, resolution and disease.
Mazouzi et al. (2014)
21 more

2 mentions without citation

Molecular underpinnings of Aprataxin RNA/DNA deadenylase function and dysfunction in neurological disease.
Schellenberg et al. (2015)
1 more