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- PDB-9qee: Cryo-EM structure of a DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP c... -

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Basic information

Entry
Database: PDB / ID: 9qee
TitleCryo-EM structure of a DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP complex
Components
  • DNA excision repair protein ERCC-1
  • DNA repair endonuclease XPF
  • DNA strand 1
  • DNA strand 2
  • Protein SLX4IP
  • Structure-specific endonuclease subunit SLX4
KeywordsHYDROLASE / DNA repair / endonuclease / multiprotein complex / DNA bound complex
Function / homology
Function and homology information


Slx1-Slx4 complex / positive regulation of t-circle formation / response to intra-S DNA damage checkpoint signaling / DNA double-strand break processing involved in repair via single-strand annealing / 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 ...Slx1-Slx4 complex / positive regulation of t-circle formation / response to intra-S DNA damage checkpoint signaling / DNA double-strand break processing involved in repair via single-strand annealing / 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 complex / negative regulation of telomere maintenance / single-stranded DNA endodeoxyribonuclease activity / resolution of meiotic recombination intermediates / telomeric D-loop disassembly / t-circle formation / mitotic recombination / post-embryonic hemopoiesis / UV protection / isotype switching / UV-damage excision repair / negative regulation of telomere maintenance via telomere lengthening / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / oogenesis / positive regulation of telomere maintenance / TFIID-class transcription factor complex binding / replicative senescence / response to X-ray / positive regulation of transcription initiation by RNA polymerase II / 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 / enzyme activator activity / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / Dual Incision in GG-NER / male gonad development / multicellular organism growth / Formation of Incision Complex in GG-NER / 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 / DNA replication / chromosome, telomeric region / cell population proliferation / regulation of autophagy / DNA repair / chromatin / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Protein SLX4IP / Uncharacterized protein family UPF0492 / Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / ERCC4 domain ...Protein SLX4IP / Uncharacterized protein family UPF0492 / Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / ERCC4 domain / ERCC4 domain / ERCC4 domain / RuvA domain 2-like / Restriction endonuclease type II-like / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Helix-hairpin-helix domain / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA excision repair protein ERCC-1 / Protein SLX4IP / Structure-specific endonuclease subunit SLX4 / DNA repair endonuclease XPF
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFeng, J. / Matthews-Palmer, T. / Greber, B.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
CitationJournal: To Be Published
Title: Molecular basis of XPF-ERCC1 targeting to SLX4-dependent DNA repair pathways
Authors: Feng, J. / Martin, P.R. / Lecot, M. / Cronin, N.B. / Matthews-Palmer, T. / Niedzwiedz, W. / Greber, B.J.
History
DepositionMar 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DNA excision repair protein ERCC-1
C: Protein SLX4IP
U: DNA strand 1
V: DNA strand 2
D: Structure-specific endonuclease subunit SLX4
A: DNA repair endonuclease XPF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,8598
Polymers245,7496
Non-polymers1102
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

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Protein , 4 types, 4 molecules BCDA

#1: 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
#2: Protein Protein SLX4IP / SLX4-interacting protein


Mass: 45627.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLX4IP, C20orf94 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5VYV7
#5: Protein Structure-specific endonuclease subunit SLX4 / BTB/POZ domain-containing protein 12


Mass: 29617.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLX4, BTBD12, KIAA1784, KIAA1987 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IY92
#6: 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

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DNA chain , 2 types, 2 molecules UV

#3: DNA chain DNA strand 1


Mass: 15425.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA strand 2


Mass: 15585.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 1 types, 2 molecules

#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn

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Details

Has ligand of interestN
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-SLX4(330-555)-SLX4IP complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.21 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 mMManganese chlorideMnCl21
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample contained a two-fold excess of DNA fork substrate over protein complex.
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: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS / Details: Fringe-free imaging used.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / C2 aperture diameter: 20 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: TFS FALCON 4i (4k x 4k) / Num. of real images: 11694
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2Topazparticle selection
3EPUimage acquisition
5cryoSPARC4.4.1CTF correction
6RELION5.0-betaCTF correction
9UCSF ChimeraXmodel fitting
11PHENIX1.21rc1_4985model refinement
12cryoSPARC4.4.1initial Euler assignment
13RELION5.0-betafinal Euler assignment
14RELION4.0-betaclassification
15RELION5.0-beta3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55779 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16SXA

6sxa

16SXA1PDBexperimental model
21AlphaFoldin silico model
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00610065
ELECTRON MICROSCOPYf_angle_d0.66213801
ELECTRON MICROSCOPYf_dihedral_angle_d18.2171611
ELECTRON MICROSCOPYf_chiral_restr0.0431587
ELECTRON MICROSCOPYf_plane_restr0.0051619

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