6SXB

XPF-ERCC1 Cryo-EM Structure, DNA-Bound form


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.90 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structures of the XPF-ERCC1 endonuclease reveal how DNA-junction engagement disrupts an auto-inhibited conformation.

Jones, M.Beuron, F.Borg, A.Nans, A.Earl, C.P.Briggs, D.C.Snijders, A.P.Bowles, M.Morris, E.P.Linch, M.McDonald, N.Q.

(2020) Nat Commun 11: 1120-1120

  • DOI: 10.1038/s41467-020-14856-2
  • Primary Citation of Related Structures:  
    6SXB, 6SXA

  • PubMed Abstract: 
  • The structure-specific endonuclease XPF-ERCC1 participates in multiple DNA damage repair pathways including nucleotide excision repair (NER) and inter-strand crosslink repair (ICLR). How XPF-ERCC1 is catalytically activated by DNA junction substrates is not currently understood ...

    The structure-specific endonuclease XPF-ERCC1 participates in multiple DNA damage repair pathways including nucleotide excision repair (NER) and inter-strand crosslink repair (ICLR). How XPF-ERCC1 is catalytically activated by DNA junction substrates is not currently understood. Here we report cryo-electron microscopy structures of both DNA-free and DNA-bound human XPF-ERCC1. DNA-free XPF-ERCC1 adopts an auto-inhibited conformation in which the XPF helical domain masks the ERCC1 (HhH) 2 domain and restricts access to the XPF catalytic site. DNA junction engagement releases the ERCC1 (HhH) 2 domain to couple with the XPF-ERCC1 nuclease/nuclease-like domains. Structure-function data indicate xeroderma pigmentosum patient mutations frequently compromise the structural integrity of XPF-ERCC1. Fanconi anaemia patient mutations in XPF often display substantial in-vitro activity but are resistant to activation by ICLR recruitment factor SLX4. Our data provide insights into XPF-ERCC1 architecture and catalytic activation.


    Organizational Affiliation

    Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK. neil.mcdonald@crick.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair endonuclease XPFA [auth F]916Homo sapiensMutation(s): 0 
Gene Names: ERCC4ERCC11XPF
EC: 3.1
Find proteins for Q92889 (Homo sapiens)
Explore Q92889 
Go to UniProtKB:  Q92889
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PHAROS:  Q92889
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-1B [auth G]297Homo sapiensMutation(s): 0 
Gene Names: ERCC1
Find proteins for P07992 (Homo sapiens)
Explore P07992 
Go to UniProtKB:  P07992
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PHAROS:  P07992
Protein Feature View
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  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*CP*AP*GP*AP*TP*GP*CP*TP*GP*A)-3')C10Homo sapiens
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    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*TP*G)-3')D10Homo sapiens
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: ELECTRON MICROSCOPY
      • Resolution: 7.90 Å
      • Aggregation State: 2D ARRAY 
      • Reconstruction Method: SINGLE PARTICLE 

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      The Francis Crick InstituteUnited Kingdom10115

      Revision History  (Full details and data files)

      • Version 1.0: 2020-03-11
        Type: Initial release