6SXA | pdb_00006sxa

XPF-ERCC1 Cryo-EM Structure, Apo-form


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6SXA

This is version 1.1 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: https://doi.org/10.1038/s41467-020-14856-2
  • Primary Citation Related Structures: 
    6SXA, 6SXB

  • 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. 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
    • Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT, London, UK.

Macromolecule Content 

  • Total Structure Weight: 137.23 kDa 
  • Atom Count: 7,014 
  • Modeled Residue Count: 943 
  • Deposited Residue Count: 1,213 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair endonuclease XPFA [auth F]916Homo sapiensMutation(s): 0 
Gene Names: ERCC4ERCC11XPF
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92889 (Homo sapiens)
Explore Q92889 
Go to UniProtKB:  Q92889
PHAROS:  Q92889
GTEx:  ENSG00000175595 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92889
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-1B [auth G]297Homo 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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2

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
  • Version 1.1: 2024-05-22
    Changes: Data collection, Database references