2N8A | pdb_00002n8a

1H, 13C and 15N chemical shift assignments and solution structure for PARP-1 F1F2 domains in complex with a DNA single-strand break


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 78 
  • Conformers Submitted: 78 
  • Selection Criteria: Total, Tensor and NOE xplor energies simultaneously below thresholds (6000, 1500 and 2 kcal.mol-1 respectively) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2N8A

This is version 1.4 of the entry. See complete history

Literature

Structural Basis of Detection and Signaling of DNA Single-Strand Breaks by Human PARP-1.

Eustermann, S.Wu, W.F.Langelier, M.F.Yang, J.C.Easton, L.E.Riccio, A.A.Pascal, J.M.Neuhaus, D.

(2015) Mol Cell 60: 742-754

  • DOI: https://doi.org/10.1016/j.molcel.2015.10.032
  • Primary Citation Related Structures: 
    2N8A

  • PubMed Abstract: 

    Poly(ADP-ribose)polymerase 1 (PARP-1) is a key eukaryotic stress sensor that responds in seconds to DNA single-strand breaks (SSBs), the most frequent genomic damage. A burst of poly(ADP-ribose) synthesis initiates DNA damage response, whereas PARP-1 inhibition kills BRCA-deficient tumor cells selectively, providing the first anti-cancer therapy based on synthetic lethality. However, the mechanism underlying PARP-1's function remained obscure; inherent dynamics of SSBs and PARP-1's multi-domain architecture hindered structural studies. Here we reveal the structural basis of SSB detection and how multi-domain folding underlies the allosteric switch that determines PARP-1's signaling response. Two flexibly linked N-terminal zinc fingers recognize the extreme deformability of SSBs and drive co-operative, stepwise self-assembly of remaining PARP-1 domains to control the activity of the C-terminal catalytic domain. Automodification in cis explains the subsequent release of monomeric PARP-1 from DNA, allowing repair and replication to proceed. Our results provide a molecular framework for understanding PARP inhibitor action and, more generally, allosteric control of dynamic, multi-domain proteins.


  • Organizational Affiliation
    • Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.

Macromolecule Content 

  • Total Structure Weight: 38.11 kDa 
  • Atom Count: 2,612 
  • Modeled Residue Count: 259 
  • Deposited Residue Count: 259 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1214Homo sapiensMutation(s): 0 
Gene Names: PARP1ADPRTPPOL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P09874 (Homo sapiens)
Explore P09874 
Go to UniProtKB:  P09874
PHAROS:  P09874
GTEx:  ENSG00000143799 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09874
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (45-MER)45N/A
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 78 
  • Conformers Submitted: 78 
  • Selection Criteria: Total, Tensor and NOE xplor energies simultaneously below thresholds (6000, 1500 and 2 kcal.mol-1 respectively) 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2015-12-23
    Changes: Database references
  • Version 1.2: 2016-10-05
    Changes: Structure summary
  • Version 1.3: 2016-10-19
    Changes: Other
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references, Derived calculations