+Open data
-Basic information
Entry | Database: PDB / ID: 6sxa | ||||||
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Title | XPF-ERCC1 Cryo-EM Structure, Apo-form | ||||||
Components |
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Keywords | DNA 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 factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair ...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 factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair complex / t-circle formation / resolution of meiotic recombination intermediates / single-stranded DNA endodeoxyribonuclease activity / response to sucrose / UV protection / mitotic recombination / 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 X-ray / response to immobilization stress / replicative senescence / positive regulation of transcription initiation by RNA polymerase II / embryonic organ development / response to cadmium ion / interstrand cross-link repair / 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 / nucleotide-excision repair / promoter-specific chromatin binding / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Jones, M.L. / Briggs, D.C. / McDonald, N.Q. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6sxa.cif.gz | 174.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sxa.ent.gz | 132.1 KB | Display | PDB format |
PDBx/mmJSON format | 6sxa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sxa_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6sxa_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6sxa_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 6sxa_validation.cif.gz | 52.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/6sxa ftp://data.pdbj.org/pub/pdb/validation_reports/sx/6sxa | HTTPS FTP |
-Related structure data
Related structure data | 10337MC 6sxbC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: 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 |
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#2: Protein | 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ERCC1/XPF complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.8 Details: 20 mM HEPES pH 7.8, 150 mM NaCl, 1 mM TCEP, 0.01% CHAPS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / 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 holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 63 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 15315 |
Image scans | Movie frames/image: 20 / Used frames/image: 2-17 |
-Processing
EM software | Name: cryoSPARC / Version: 2 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 405339 / Num. of class averages: 1 / Symmetry type: POINT |