9QEC | pdb_00009qec

Cryo-EM structure of the XPF-ERCC1-XPA complex

• PDB DOI: https://doi.org/10.2210/pdb9QEC/pdb
• EM Map EMD-53054: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-03-08 Released: 2025-12-17 
• Deposition Author(s): Feng, J., Cronin, N.B., Greber, B.J.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 170.91 kDa 
• Atom Count: 7,688 
• Modeled Residue Count: 959 
• Deposited Residue Count: 1,505 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair endonuclease XPF	A	935	Homo sapiens	Mutation(s): 0  Gene Names: ERCC4, ERCC11, XPF 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA excision repair protein ERCC-1	B	297	Homo sapiens	Mutation(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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein complementing XP-A cells	C	273	Homo sapiens	Mutation(s): 0  Gene Names: XPA, XPAC
UniProt & NIH Common Fund Data Resources
Find proteins for P23025 (Homo sapiens) Explore P23025  Go to UniProtKB:  P23025
PHAROS:  P23025 GTEx:  ENSG00000136936

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0-beta
MODEL REFINEMENT	PHENIX	1.21rc1_4985

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Feng, J., Cronin, N.B., Greber, B.J.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/V009354/1

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release