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

X-ray diffraction
3.25Å resolution
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
Assembly composition:
hetero pentamer (preferred)
Entry contents: 3 distinct polypeptide molecules
1 distinct DNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Poly [ADP-ribose] polymerase 1, processed C-terminus and DNA
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Multimeric state: hetero pentamer
Accessible surface area: 43011.61 Å2
Buried surface area: 6681.73 Å2
Dissociation area: 2,026.71 Å2
Dissociation energy (ΔGdiss): -5.23 kcal/mol
Dissociation entropy (TΔSdiss): 36.72 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117342
Assembly 2
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Assembly Name: Poly [ADP-ribose] polymerase 1, processed C-terminus and DNA
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Multimeric state: hetero pentamer
Accessible surface area: 43175.98 Å2
Buried surface area: 6187.2 Å2
Dissociation area: 1,961.04 Å2
Dissociation energy (ΔGdiss): -5.84 kcal/mol
Dissociation entropy (TΔSdiss): 36.7 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117342

Macromolecules

Poly [ADP-ribose] polymerase 1, processed N-terminus
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
Pfam: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
InterPro:
CATH: Zinc finger, PARP-type
Poly [ADP-ribose] polymerase 1, processed N-terminus in PDB entry 4dqy, assembly 1, front view.
Poly [ADP-ribose] polymerase 1, processed N-terminus in PDB entry 4dqy, assembly 1, side view.
Poly [ADP-ribose] polymerase 1, processed N-terminus in PDB entry 4dqy, assembly 1, top view.
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Poly [ADP-ribose] polymerase 1, processed C-terminus
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
Pfam:
InterPro:
CATH:
Poly [ADP-ribose] polymerase 1, processed C-terminus in PDB entry 4dqy, assembly 1, front view.
Poly [ADP-ribose] polymerase 1, processed C-terminus in PDB entry 4dqy, assembly 1, side view.
Poly [ADP-ribose] polymerase 1, processed C-terminus in PDB entry 4dqy, assembly 1, top view.
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Poly [ADP-ribose] polymerase 1, processed C-terminus
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
Pfam:
InterPro:
CATH:
Poly [ADP-ribose] polymerase 1, processed C-terminus in PDB entry 4dqy, assembly 1, front view.
Poly [ADP-ribose] polymerase 1, processed C-terminus in PDB entry 4dqy, assembly 1, side view.
Poly [ADP-ribose] polymerase 1, processed C-terminus in PDB entry 4dqy, assembly 1, top view.
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DNA chains M, N
Name: DNA (26-MER)
Representative chains: M, N
Length: 26 nucleotides
Theoretical weight: 7.99 KDa
DNA (26-MER) in PDB entry 4dqy, assembly 1, front view.
DNA (26-MER) in PDB entry 4dqy, assembly 1, side view.
DNA (26-MER) in PDB entry 4dqy, assembly 1, top view.
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