2JPD | pdb_00002jpd

Solution structure of the ERCC1 central domain


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Analysis of the XPA and ssDNA-binding surfaces on the central domain of human ERCC1 reveals evidence for subfunctionalization

Tripsianes, K.Folkers, G.E.Zheng, C.Das, D.Grinstead, J.S.Kaptein, R.Boelens, R.

(2007) Nucleic Acids Res 35: 5789-5798

  • DOI: https://doi.org/10.1093/nar/gkm503
  • Primary Citation Related Structures: 
    2JPD

  • PubMed Abstract: 

    Human ERCC1/XPF is a structure-specific endonuclease involved in multiple DNA repair pathways. We present the solution structure of the non-catalytic ERCC1 central domain. Although this domain shows structural homology with the catalytically active XPF nuclease domain, functional investigation reveals a completely distinct function for the ERCC1 central domain by performing interactions with both XPA and single-stranded DNA. These interactions are non-competitive and can occur simultaneously through distinct interaction surfaces. Interestingly, the XPA binding by ERCC1 and the catalytic function of XPF are dependent on a structurally homologous region of the two proteins. Although these regions are strictly conserved in each protein family, amino acid composition and surface characteristics are distinct. We discuss the possibility that after XPF gene duplication, the redundant ERCC1 central domain acquired novel functions, thereby increasing the fidelity of eukaryotic DNA repair.


  • Organizational Affiliation
    • Department of NMR spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 15.46 kDa 
  • Atom Count: 996 
  • Modeled Residue Count: 124 
  • Deposited Residue Count: 135 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-1135Homo sapiensMutation(s): 0 
Gene Names: ERCC1
UniProt & NIH Common Fund Data Resources
Find proteins for P07992 (Homo sapiens)
Explore P07992 
Go to UniProtKB:  P07992
PHAROS:  P07992
GTEx:  ENSG00000012061 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07992
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-05
    Changes: Data collection, Database references, Derived calculations, Experimental preparation, Other
  • Version 1.3: 2023-06-14
    Changes: Database references, Other
  • Version 1.4: 2023-12-20
    Changes: Data collection, Other
  • Version 1.5: 2024-05-08
    Changes: Database references