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- PDB-9qec: Cryo-EM structure of the XPF-ERCC1-XPA complex -

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Basic information

Entry
Database: PDB / ID: 9qec
TitleCryo-EM structure of the XPF-ERCC1-XPA complex
Components
  • DNA excision repair protein ERCC-1
  • DNA repair endonuclease XPF
  • DNA repair protein complementing XP-A cells
KeywordsHYDROLASE / DNA repair / endonuclease / multiprotein complex
Function / homology
Function and homology information


positive regulation of t-circle formation / pyrimidine dimer repair by nucleotide-excision repair / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / syncytium formation / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair complex ...positive regulation of t-circle formation / pyrimidine dimer repair by nucleotide-excision repair / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / syncytium formation / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair complex / negative regulation of telomere maintenance / single-stranded DNA endodeoxyribonuclease activity / resolution of meiotic recombination intermediates / t-circle formation / mitotic recombination / post-embryonic hemopoiesis / UV protection / isotype switching / UV-damage excision repair / negative regulation of telomere maintenance via telomere lengthening / HDR through Single Strand Annealing (SSA) / oogenesis / TFIID-class transcription factor complex binding / replicative senescence / response to X-ray / positive regulation of transcription initiation by RNA polymerase II / protein localization to nucleus / interstrand cross-link repair / response to UV / insulin-like growth factor receptor signaling pathway / telomere maintenance / determination of adult lifespan / DNA endonuclease activity / nucleotide-excision repair / promoter-specific chromatin binding / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / base-excision repair / regulation of autophagy / double-strand break repair via nonhomologous end joining / response to toxic substance / male gonad development / Dual Incision in GG-NER / multicellular organism growth / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / Dual incision in TC-NER / cellular response to UV / single-stranded DNA binding / response to oxidative stress / spermatogenesis / damaged DNA binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / cell population proliferation / nuclear body / protein domain specific binding / DNA repair / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / XPA protein N-terminal / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site ...DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / XPA protein N-terminal / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus / XPA protein signature 1. / XPA protein signature 2. / XPA domain superfamily / ERCC4 domain / ERCC4 domain / ERCC4 domain / Putative DNA-binding domain superfamily / RuvA domain 2-like / Restriction endonuclease type II-like / Helix-hairpin-helix domain
Similarity search - Domain/homology
DNA excision repair protein ERCC-1 / DNA repair protein complementing XP-A cells / DNA repair endonuclease XPF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFeng, J. / Cronin, N.B. / Greber, B.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Molecular basis of XPF-ERCC1 targeting to SLX4-dependent DNA repair pathways.
Authors: Junjie Feng / Peter R Martin / Szymon Kowalski / Maxime Lecot / Nora B Cronin / Teige Matthews-Palmer / Wojciech Niedzwiedz / Basil J Greber /
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 ...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 complex with DNA bound at its active site, and they complete the structural characterisation of molecular interactions required to assemble the SMX complex.
History
DepositionMar 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair endonuclease XPF
B: DNA excision repair protein ERCC-1
C: DNA repair protein complementing XP-A cells


Theoretical massNumber of molelcules
Total (without water)170,9153
Polymers170,9153
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein DNA repair endonuclease XPF / DNA excision repair protein ERCC-4 / DNA repair protein complementing XP-F cells / Xeroderma ...DNA excision repair protein ERCC-4 / DNA repair protein complementing XP-F cells / Xeroderma pigmentosum group F-complementing protein


Mass: 106894.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC4, ERCC11, XPF / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q92889, Hydrolases; Acting on ester bonds
#2: Protein DNA excision repair protein ERCC-1


Mass: 32598.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07992
#3: Protein DNA repair protein complementing XP-A cells / Xeroderma pigmentosum group A-complementing protein


Mass: 31422.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPA, XPAC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P23025
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: XPF-ERCC1-XPA complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.17 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.9
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES-KOH1
2200 mMPotassium chlorideKCl1
32 mMMagnesium chlorideMgCl21
45 mMbeta-mercaptoethanol1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 12629
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2Topazparticle selection
3EPUimage acquisition
5cryoSPARC3.3.1CTF correction
6RELION4.0-betaCTF correction
9UCSF ChimeraXmodel fitting
11cryoSPARC3.3.1initial Euler assignment
12RELION4.0-betafinal Euler assignment
13RELION4.0-betaclassification
14RELION4.0-beta3D reconstruction
15PHENIX1.21rc1_4985model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73737 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6SXA

6sxa


Accession code: 6SXA / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027843
ELECTRON MICROSCOPYf_angle_d0.47810619
ELECTRON MICROSCOPYf_dihedral_angle_d3.4811043
ELECTRON MICROSCOPYf_chiral_restr0.0381220
ELECTRON MICROSCOPYf_plane_restr0.0041353

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