2KN7

Structure of the XPF-single strand DNA complex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition

Das, D.Folkers, G.E.van Dijk, M.Jaspers, N.G.J.Hoeijmakers, J.H.J.Kaptein, R.Boelens, R.

(2012) Structure 20: 667-675

  • DOI: 10.1016/j.str.2012.02.009
  • Primary Citation of Related Structures:  
    2KN7

  • PubMed Abstract: 
  • Human XPF/ERCC1 is a structure-specific DNA endonuclease that nicks the damaged DNA strand at the 5' end during nucleotide excision repair. We determined the structure of the complex of the C-terminal domain of XPF with 10 nt ssDNA. A positively charged ...

    Human XPF/ERCC1 is a structure-specific DNA endonuclease that nicks the damaged DNA strand at the 5' end during nucleotide excision repair. We determined the structure of the complex of the C-terminal domain of XPF with 10 nt ssDNA. A positively charged region within the second helix of the first HhH motif contacts the ssDNA phosphate backbone. One guanine base is flipped out of register and positioned in a pocket contacting residues from both HhH motifs of XPF. Comparison to other HhH-containing proteins indicates a one-residue deletion in the second HhH motif of XPF that has altered the hairpin conformation, thereby permitting ssDNA interactions. Previous nuclear magnetic resonance studies showed that ERCC1 in the XPF-ERCC1 heterodimer can bind dsDNA. Combining the two observations gives a model that underscores the asymmetry of the human XPF/ERCC1 heterodimer in binding at an ss/ds DNA junction.


    Organizational Affiliation

    Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair endonuclease XPF AD67Homo sapiensMutation(s): 0 
Gene Names: XPFERCC4ERCC11
EC: 3.1
Find proteins for Q92889 (Homo sapiens)
Explore Q92889 
Go to UniProtKB:  Q92889
NIH Common Fund Data Resources
PHAROS:  Q92889
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*AP*GP*TP*GP*GP*CP*TP*GP*A)-3')B, C10N/A
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Calculated: 200 
    • Conformers Submitted: 20 
    • Selection Criteria: structures with the lowest energy 
    • OLDERADO: 2KN7 Olderado

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2010-08-04
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance
    • Version 1.2: 2012-07-04
      Changes: Database references