4DQY

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Structural basis for DNA damage-dependent poly(ADP-ribosyl)ation by human PARP-1.

Langelier, M.F., Planck, J.L., Roy, S., Pascal, J.M.

(2012) Science 336: 728-732

  • DOI: 10.1126/science.1216338

  • PubMed Abstract: 

    • Poly(ADP-ribose) polymerase-1 (PARP-1) (ADP, adenosine diphosphate) has a modular domain architecture that couples DNA damage detection to poly(ADP-ribosyl)ation activity through a poorly understood mechanism. Here, we report the crystal structure of ...

    Poly(ADP-ribose) polymerase-1 (PARP-1) (ADP, adenosine diphosphate) has a modular domain architecture that couples DNA damage detection to poly(ADP-ribosyl)ation activity through a poorly understood mechanism. Here, we report the crystal structure of a DNA double-strand break in complex with human PARP-1 domains essential for activation (Zn1, Zn3, WGR-CAT). PARP-1 engages DNA as a monomer, and the interaction with DNA damage organizes PARP-1 domains into a collapsed conformation that can explain the strong preference for automodification. The Zn1, Zn3, and WGR domains collectively bind to DNA, forming a network of interdomain contacts that links the DNA damage interface to the catalytic domain (CAT). The DNA damage-induced conformation of PARP-1 results in structural distortions that destabilize the CAT. Our results suggest that an increase in CAT protein dynamics underlies the DNA-dependent activation mechanism of PARP-1.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, The Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly [ADP-ribose] polymerase 1
A, D
116Homo sapiensMutation(s): 0 
Gene Names: PARP1 (ADPRT, PPOL)
EC: 2.4.2.30
Find proteins for P09874 (Homo sapiens)
Go to Gene View: PARP1
Go to UniProtKB:  P09874
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Poly [ADP-ribose] polymerase 1
B, E
160Homo sapiensMutation(s): 0 
Gene Names: PARP1 (ADPRT, PPOL)
EC: 2.4.2.30
Find proteins for P09874 (Homo sapiens)
Go to Gene View: PARP1
Go to UniProtKB:  P09874
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Poly [ADP-ribose] polymerase 1
C, F
506Homo sapiensMutation(s): 0 
Gene Names: PARP1 (ADPRT, PPOL)
EC: 2.4.2.30
Find proteins for P09874 (Homo sapiens)
Go to Gene View: PARP1
Go to UniProtKB:  P09874
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (26-MER)M,N26N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, D, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.095α = 90.00
b = 112.965β = 90.00
c = 294.724γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
CBASSdata collection
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release