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- PDB-6sxa: XPF-ERCC1 Cryo-EM Structure, Apo-form -

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Basic information

Entry
Database: PDB / ID: 6sxa
TitleXPF-ERCC1 Cryo-EM Structure, Apo-form
Components
  • DNA excision repair protein ERCC-1
  • DNA repair endonuclease XPF
KeywordsDNA BINDING PROTEIN / DNA Repair enzyme. Nucleotide excision repair
Function / homology
Function and homology information


negative regulation of double-stranded telomeric DNA binding / positive regulation of t-circle formation / negative regulation of telomere maintenance / 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 involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex ...negative regulation of double-stranded telomeric DNA binding / positive regulation of t-circle formation / negative regulation of telomere maintenance / 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 involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / nucleotide-excision repair complex / t-circle formation / single-stranded DNA endodeoxyribonuclease activity / response to sucrose / resolution of meiotic recombination intermediates / mitotic recombination / UV protection / post-embryonic hemopoiesis / 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 / response to immobilization stress / response to X-ray / replicative senescence / positive regulation of transcription initiation by RNA polymerase II / embryonic organ development / interstrand cross-link repair / response to cadmium ion / response to UV / telomere maintenance / response to nutrient / insulin-like growth factor receptor signaling pathway / DNA endonuclease activity / regulation of autophagy / determination of adult lifespan / promoter-specific chromatin binding / nucleotide-excision repair / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / multicellular organism growth / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / double-strand break repair via nonhomologous end joining / Dual incision in TC-NER / male gonad development / cellular response to UV / single-stranded DNA binding / spermatogenesis / response to oxidative stress / cell population proliferation / damaged DNA binding / chromosome, telomeric region / Hydrolases; Acting on ester bonds / DNA repair / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / Rossmann fold - #10130 / ERCC4 domain / ERCC4 domain / ERCC4 domain / Helix-hairpin-helix motif ...DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / Rossmann fold - #10130 / ERCC4 domain / ERCC4 domain / ERCC4 domain / Helix-hairpin-helix motif / RuvA domain 2-like / Restriction endonuclease type II-like / Helix-hairpin-helix domain / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA excision repair protein ERCC-1 / DNA repair endonuclease XPF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsJones, M.L. / Briggs, D.C. / McDonald, N.Q.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick Institute10115 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structures of the XPF-ERCC1 endonuclease reveal how DNA-junction engagement disrupts an auto-inhibited conformation.
Authors: Morgan Jones / Fabienne Beuron / Aaron Borg / Andrea Nans / Christopher P Earl / David C Briggs / Ambrosius P Snijders / Maureen Bowles / Edward P Morris / Mark Linch / Neil Q McDonald /
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 ...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) domain and restricts access to the XPF catalytic site. DNA junction engagement releases the ERCC1 (HhH) 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.
History
DepositionSep 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
F: DNA repair endonuclease XPF
G: DNA excision repair protein ERCC-1


Theoretical massNumber of molelcules
Total (without water)137,2342
Polymers137,2342
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry, Crosslinking Mass Spec
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5980 Å2
ΔGint-44 kcal/mol
Surface area49040 Å2
MethodPISA

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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: 104636.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC4, ERCC11, XPF / 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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07992

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ERCC1/XPF complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.8
Details: 20 mM HEPES pH 7.8, 150 mM NaCl, 1 mM TCEP, 0.01% CHAPS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4200 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 900 nm / Calibrated defocus max: 4500 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 63 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 15315
Image scansMovie frames/image: 20 / Used frames/image: 2-17

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Processing

EM softwareName: cryoSPARC / Version: 2 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 405339 / Num. of class averages: 1 / Symmetry type: POINT

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