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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10338 | |||||||||
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Title | XPF-ERCC1 Cryo-EM Structure, DNA-Bound form | |||||||||
![]() | Sharpened map | |||||||||
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![]() | DNA Repair enzyme. Nucleotide excision repair / DNA BINDING PROTEIN | |||||||||
Function / homology | ![]() negative regulation of double-stranded telomeric DNA binding / double-strand break repair via single-strand annealing, removal of nonhomologous ends / 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 ...negative regulation of double-stranded telomeric DNA binding / double-strand break repair via single-strand annealing, removal of nonhomologous ends / 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 / response to sucrose / single-stranded DNA endodeoxyribonuclease activity / UV protection / post-embryonic hemopoiesis / isotype switching / mitotic recombination / 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 / chromosome, telomeric region / damaged DNA binding / Hydrolases; Acting on ester bonds / DNA repair / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.9 Å | |||||||||
![]() | Jones ML / Briggs DC | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 20.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.6 KB 15.6 KB | Display Display | ![]() |
Images | ![]() | 57.3 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 493.1 KB | Display | ![]() |
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Full document | ![]() | 492.7 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6sxbMC ![]() 6sxaC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : ERCC1/XPF/DNA complex
Entire | Name: ERCC1/XPF/DNA complex |
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Components |
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-Supramolecule #1: ERCC1/XPF/DNA complex
Supramolecule | Name: ERCC1/XPF/DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: ERCC1/XPF
Supramolecule | Name: ERCC1/XPF / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: DNA repair endonuclease XPF
Macromolecule | Name: DNA repair endonuclease XPF / type: protein_or_peptide / ID: 1 Details: Some residues have been modelled as Alanine where sidechains were not visible. Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 104.636156 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MESGQPARRI AMAPLLEYER QLVLELLDTD GLVVCARGLG ADRLLYHFLQ LHCHPACLVL VLNTQPAEEE YFINQLKIEG VEHLPRRVT NEITSNSRYE VYTQGGVIFA TSRILVVDFL TDRIPSDLIT GILVYRAHRI IESCQEAFIL RLFRQKNKRG F IKAFTDNA ...String: MESGQPARRI AMAPLLEYER QLVLELLDTD GLVVCARGLG ADRLLYHFLQ LHCHPACLVL VLNTQPAEEE YFINQLKIEG VEHLPRRVT NEITSNSRYE VYTQGGVIFA TSRILVVDFL TDRIPSDLIT GILVYRAHRI IESCQEAFIL RLFRQKNKRG F IKAFTDNA VAFDTGFCHV ERVMRNLFVR KLYLWPRFHV AVNSFLEQHK PEVVEIHVSM TPTMLAIQTA ILDILNACLK EL KCHNPSL EVEDLSLENA IGKPFDKTIR HYLDPLWHQL GAKTKSLVQD LKILRTLLQY LSQYDCVTFL NLLESLRATE KAF GQNSGW LFLDSSTSMF INARARVYHL PDAKMSKKEK ISEKMEIKEG EETKKELVLE SNPKWEALTE VLKEIEAENK ESEA LGGPG QVLICASDDR TCSQLRDYIT LGAEAFLLRL YRKTFEKDSK AEEVWMKFRK EDSSKRIRKS HKRPKDPQNK ERAST KERT LKKKKRKLTL TQMVGKPEEL EEEGDVEEGY RREISSSPES CPEEIKHEEF DVNLSSDAAF GILKEPLTII HPLLGC SDP YALTRVLHEV EPRYVVLYDA ELTFVRQLEI YRASRPGKPL RVYFLIYGGS TEEQRYLTAL RKEKEAFEKL IREKASM VV PEEREGRDET NLDLVRGTAS ADVSTDTRKA GGQEQNGTQQ SIVVDMREFR SELPSLIHRR GIDIEPVTLE VGDYILTP E MCVERKSISD LIGSLNNGRL YSQCISMSRY YKRPVLLIEF DPSKPFSLTS RGALFQEISS NDISSKLTLL TLHFPRLRI LWCPSPHATA ELFEELKQSK PQPDAATALA ITADSETLPE SEKYNPGPQD FLLKMPGVNA KNCRSLMHHV KNIAELAALS QDELTSILG NAANAKQLYD FIHTSFAEVV SKGKGKK UniProtKB: DNA repair endonuclease XPF |
-Macromolecule #2: DNA excision repair protein ERCC-1
Macromolecule | Name: DNA excision repair protein ERCC-1 / type: protein_or_peptide / ID: 2 Details: Some residues modelled as Alanine where no sidechain information available. Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 32.598301 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVAKPLF RSTQSLPTVD TSAQAAPQTY AEYAISQPLE GAGATCPTGS EPLAGETPN QALKPGAKSN SIIVSPRQRG NPVLKFVRNV PWEFGDVIPD YVLGQSTCAL FLSLRYHNLH PDYIHGRLQS L GKNFALRV ...String: MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVAKPLF RSTQSLPTVD TSAQAAPQTY AEYAISQPLE GAGATCPTGS EPLAGETPN QALKPGAKSN SIIVSPRQRG NPVLKFVRNV PWEFGDVIPD YVLGQSTCAL FLSLRYHNLH PDYIHGRLQS L GKNFALRV LLVQVDVKDP QQALKELAKM CILADCTLIL AWSPEEAGRY LETYKAYEQK PADLLMEKLE QDFVSRVTEC LT TVKSVNK TDSQTLLTTF GSLEQLIAAS REDLALCPGL GPQKARRLFD VLHEPFLKVP UniProtKB: DNA excision repair protein ERCC-1 |
-Macromolecule #3: DNA (5'-D(P*CP*AP*GP*AP*TP*GP*CP*TP*GP*A)-3')
Macromolecule | Name: DNA (5'-D(P*CP*AP*GP*AP*TP*GP*CP*TP*GP*A)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 3.06903 KDa |
Sequence | String: (DC)(DA)(DG)(DA)(DT)(DG)(DC)(DT)(DG)(DA) |
-Macromolecule #4: DNA (5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*TP*G)-3')
Macromolecule | Name: DNA (5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*TP*G)-3') / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 3.019992 KDa |
Sequence | String: (DT)(DC)(DA)(DG)(DC)(DA)(DT)(DC)(DT)(DG) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | 2D array |
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Sample preparation
Buffer | pH: 7.8 Details: 20 mM HEPES pH 7.8, 150 mM NaCl, 1 mM TCEP, 0.01% CHAPS |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-17 / Number real images: 15315 / Average electron dose: 63.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 4.5 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.2 µm / Nominal defocus min: 1.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 198212 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |