9QEE | pdb_00009qee

Cryo-EM structure of a DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis of XPF-ERCC1 targeting to SLX4-dependent DNA repair pathways.

Feng, J.Martin, P.R.Kowalski, S.Lecot, M.Cronin, N.B.Matthews-Palmer, T.Niedzwiedz, W.Greber, B.J.

(2025) Nat Commun 17: 522-522

  • DOI: https://doi.org/10.1038/s41467-025-67216-3
  • Primary Citation of Related Structures:  
    9QEC, 9QED, 9QEE

  • PubMed Abstract: 

    The preservation and faithful propagation of genetic information is essential for all life forms and depends on cellular pathways that enable replication, recombination, and repair of DNA. The multifunctional XPF-ERCC1 DNA endonuclease complex acts in several DNA repair pathways and interacts with numerous partner proteins and large DNA repair assemblies, including the nucleotide excision repair machinery and the SMX tri-endonuclease complex. Here, we report structures of XPF-ERCC1 in complex with the DNA repair factors SLX4 and SLX4IP, thereby identifying key residues responsible for direct interactions with XPF-ERCC1. When introduced into human cells, point mutations in these interfaces impair the interactions between XPF-ERCC1 and SLX4 or SLX4IP, and disruption of the XPF-SLX4IP interface leads to cis-platin sensitivity. Furthermore, our data reveal the structure of the human XPF-ERCC1-SLX4IP-SLX4 330-555 complex with DNA bound at its active site, and they complete the structural characterisation of molecular interactions required to assemble the SMX complex.


  • Organizational Affiliation
    • Division of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories, London, UK.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-1A [auth B]297Homo sapiensMutation(s): 0 
Gene Names: ERCC1
UniProt & NIH Common Fund Data Resources
Find proteins for P07992 (Homo sapiens)
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Go to UniProtKB:  P07992
PHAROS:  P07992
GTEx:  ENSG00000012061 
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UniProt GroupP07992
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SLX4IPB [auth C]408Homo sapiensMutation(s): 0 
Gene Names: SLX4IPC20orf94
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VYV7 (Homo sapiens)
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Go to UniProtKB:  Q5VYV7
PHAROS:  Q5VYV7
GTEx:  ENSG00000149346 
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UniProt GroupQ5VYV7
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Structure-specific endonuclease subunit SLX4E [auth D]271Homo sapiensMutation(s): 0 
Gene Names: SLX4BTBD12KIAA1784KIAA1987
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Find proteins for Q8IY92 (Homo sapiens)
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Go to UniProtKB:  Q8IY92
PHAROS:  Q8IY92
GTEx:  ENSG00000188827 
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UniProt GroupQ8IY92
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair endonuclease XPFF [auth A]935Homo sapiensMutation(s): 0 
Gene Names: ERCC4ERCC11XPF
EC: 3.1
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Find proteins for Q92889 (Homo sapiens)
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PHAROS:  Q92889
GTEx:  ENSG00000175595 
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UniProt GroupQ92889
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA strand 1C [auth U]50synthetic construct
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA strand 2D [auth V]50synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_4985
RECONSTRUCTIONRELION5.0-beta

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/V009354/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Data collection, Database references
  • Version 1.2: 2026-01-28
    Changes: Data collection, Database references