› 4dqy

X-ray diffraction
3.25Å resolution

Structure of Human PARP-1 bound to a DNA double strand break

Released:
DOI: 10.2210/pdb4dqy/pdb
PDB entry 4dqy coloured by chain, front view.
PDB entry 4dqy coloured by chain, side view.
PDB entry 4dqy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for DNA damage-dependent poly(ADP-ribosyl)ation by human PARP-1.
Langelier MF, Planck JL, Roy S, Pascal JM
Science 336 728-32 (2012)
PMID: 22582261

Function and Biology Details

Reaction catalysed: 
NAD(+) + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117342 (preferred)
Entry contents:
3 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (4 distinct):
Poly [ADP-ribose] polymerase 1, processed N-terminus Chains: A, D
Molecule details ›
Chains: A, D
Length: 116 amino acids
Theoretical weight: 13.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09874 (Residues: 1-96; Coverage: 10%)
Gene names: ADPRT, PARP1, PPOL
Sequence domains: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
Structure domains: Zinc finger, PARP-type
Poly [ADP-ribose] polymerase 1, processed C-terminus Chains: B, E
Molecule details ›
Chains: B, E
Length: 160 amino acids
Theoretical weight: 18.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09874 (Residues: 216-366; Coverage: 15%)
Gene names: ADPRT, PARP1, PPOL
Sequence domains:
Structure domains:
Poly [ADP-ribose] polymerase 1, processed C-terminus Chains: C, F
Molecule details ›
Chains: C, F
Length: 506 amino acids
Theoretical weight: 57.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09874 (Residues: 518-1014; Coverage: 49%)
Gene names: ADPRT, PARP1, PPOL
Sequence domains:
Structure domains:
DNA (26-MER) Chains: M, N
Molecule details ›
Chains: M, N
Length: 26 nucleotides
Theoretical weight: 7.99 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 65.095Å b: 112.965Å c: 294.724Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.242 0.238 0.304
Expression system: Escherichia coli

Quick links

Citations

120 review citations

New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs.
Gibson et al. (2012)
119 more

54 mentions without citation

PARP-1 mechanism for coupling DNA damage detection to poly(ADP-ribose) synthesis.
Langelier et al. (2013)
53 more