2BHN

XPF from Aeropyrum pernix


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.216 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
XPF ENDONUCLEASE
A, B, C, D
214Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)Mutation(s): 0 
Find proteins for Q9YC15 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Go to UniProtKB:  Q9YC15
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 210.325α = 90.00
b = 42.752β = 121.42
c = 118.736γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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