2BGW

XPF from Aeropyrum pernix, complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition.

Newman, M.Murray-Rust, J.Lally, J.Rudolf, J.Fadden, A.Knowles, P.P.White, M.F.McDonald, N.Q.

(2005) EMBO J 24: 895-905

  • DOI: 10.1038/sj.emboj.7600581
  • Primary Citation of Related Structures:  
    2BHN, 2BGW

  • PubMed Abstract: 
  • The XPF/Mus81 structure-specific endonucleases cleave double-stranded DNA (dsDNA) within asymmetric branched DNA substrates and play an essential role in nucleotide excision repair, recombination and genome integrity. We report the structure of an ar ...

    The XPF/Mus81 structure-specific endonucleases cleave double-stranded DNA (dsDNA) within asymmetric branched DNA substrates and play an essential role in nucleotide excision repair, recombination and genome integrity. We report the structure of an archaeal XPF homodimer alone and bound to dsDNA. Superposition of these structures reveals a large domain movement upon binding DNA, indicating how the (HhH)(2) domain and the nuclease domain are coupled to allow the recognition of double-stranded/single-stranded DNA junctions. We identify two nonequivalent DNA-binding sites and propose a model in which XPF distorts the 3' flap substrate in order to engage both binding sites and promote strand cleavage. The model rationalises published biochemical data and implies a novel role for the ERCC1 subunit of eukaryotic XPF complexes.


    Organizational Affiliation

    Structural Biology Laboratory, London Research Institute, Cancer Research UK, London, UK.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
XPF ENDONUCLEASEAB219Aeropyrum pernixMutation(s): 0 
EC: 2.7.7
Find proteins for Q9YC15 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9YC15 
Go to UniProtKB:  Q9YC15
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*AP*TP*CP*AP*CP*AP*GP*AP*TP *GP*CP*TP*GP*A)-3'C15synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*TP*GP *TP*GP*AP*TP*C)-3'D15synthetic construct
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SO4
      Query on SO4

      Download CCD File 
      A, B, D
      SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L
       Ligand Interaction
      MG
      Query on MG

      Download CCD File 
      A
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.80 Å
      • R-Value Free: 0.263 
      • R-Value Work: 0.223 
      • R-Value Observed: 0.225 
      • Space Group: P 32 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 141.312α = 90
      b = 141.312β = 90
      c = 85.311γ = 120
      Software Package:
      Software NamePurpose
      REFMACrefinement
      MOSFLMdata reduction
      SCALAdata scaling
      MOLREPphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2005-02-23
        Type: Initial release
      • Version 1.1: 2011-05-08
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2018-03-14
        Changes: Database references, Source and taxonomy, Structure summary
      • Version 1.4: 2019-05-08
        Changes: Data collection, Experimental preparation