3K77 | pdb_00003k77

X-ray crystal structure of XRCC1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.237 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

Oxidation state of the XRCC1 N-terminal domain regulates DNA polymerase beta binding affinity.

Cuneo, M.J., London, R.E.

(2010) Proc Natl Acad Sci U S A 107: 6805-6810

  • DOI: https://doi.org/10.1073/pnas.0914077107
  • Primary Citation Related Structures: 
    3K75, 3K77, 3LQC

  • PubMed Abstract: 

    Formation of a complex between the XRCC1 N-terminal domain (NTD) and DNA polymerase beta (Pol beta) is central to base excision repair of damaged DNA. Two crystal forms of XRCC1-NTD complexed with Pol beta have been solved, revealing that the XRCC1-NTD is able to adopt a redox-dependent alternate fold, characterized by a disulfide bond, and substantial variations of secondary structure, folding topology, and electrostatic surface. Although most of these structural changes occur distal to the interface, the oxidized XRCC1-NTD forms additional interactions with Pol beta, enhancing affinity by an order of magnitude. Transient disulfide bond formation is increasingly recognized as an important molecular regulatory mechanism. The results presented here suggest a paradigm in DNA repair in which the redox state of a scaffolding protein plays an active role in organizing the repair complex.

    • Organizational Affiliation: 
    • Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.

Macromolecule Content 

  • Total Structure Weight: 143.75 kDa 
  • Atom Count: 9,492 
  • Modeled Residue Count: 1,216 
  • Deposited Residue Count: 1,288 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair protein XRCC1
A, B, C, D, E
A, B, C, D, E, F, G, H
161Homo sapiensMutation(s): 0 
Gene Names: XRCC1
UniProt & NIH Common Fund Data Resources
Find proteins for P18887 (Homo sapiens)
Explore P18887 
Go to UniProtKB:  P18887
PHAROS:  P18887
GTEx:  ENSG00000073050 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18887
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.237 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.451α = 90
b = 89.302β = 90.03
c = 93.178γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Refinement description