› 6cvq

X-ray diffraction
1.65Å resolution

Human Aprataxin (Aptx) H201Q bound to RNA-DNA, AMP and Zn product complex

Released:
DOI: 10.2210/pdb6cvq/pdb
PDB entry 6cvq coloured by chain, front view.
PDB entry 6cvq coloured by chain, side view.
PDB entry 6cvq 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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113211 (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: 180 amino acids
Theoretical weight: 21.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7Z2E3 (Residues: 179-354; Coverage: 49%)
Gene names: APTX, AXA1
Sequence domains:
Structure domains: HIT-like
DNA (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
DNA/RNA (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 GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 40.571Å b: 116.049Å c: 117.215Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.12 0.118 0.168
Expression systems:
  • Escherichia coli BL21(DE3)
  • 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

1 mention without citation

Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease.
Tumbale et al. (2018)