[English] 日本語
Yorodumi
- PDB-6sxb: XPF-ERCC1 Cryo-EM Structure, DNA-Bound form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sxb
TitleXPF-ERCC1 Cryo-EM Structure, DNA-Bound form
Components
  • DNA (5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*TP*G)-3')
  • DNA (5'-D(P*CP*AP*GP*AP*TP*GP*CP*TP*GP*A)-3')
  • 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 / 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 / negative regulation of telomere maintenance / 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 / 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 / negative regulation of telomere maintenance / syncytium formation / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / nucleotide-excision repair complex / response to sucrose / t-circle formation / single-stranded DNA endodeoxyribonuclease activity / 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 / promoter-specific chromatin binding / determination of adult lifespan / 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
DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / ERCC4 domain / ERCC4 domain / ERCC4 domain / Helix-hairpin-helix motif / RuvA domain 2-like ...DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / ERCC4 domain / ERCC4 domain / ERCC4 domain / Helix-hairpin-helix motif / RuvA domain 2-like / Restriction endonuclease type II-like / Helix-hairpin-helix domain
Similarity search - Domain/homology
DNA / 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: 7.9 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-10338
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: DNA repair endonuclease XPF
G: DNA excision repair protein ERCC-1
C: DNA (5'-D(P*CP*AP*GP*AP*TP*GP*CP*TP*GP*A)-3')
D: DNA (5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)143,3234
Polymers143,3234
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7940 Å2
ΔGint-47 kcal/mol
Surface area51360 Å2
MethodPISA

-
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
Details: Some residues have been modelled as Alanine where sidechains were not visible.
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
Details: Some residues modelled as Alanine where no sidechain information available.
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07992
#3: DNA chain DNA (5'-D(P*CP*AP*GP*AP*TP*GP*CP*TP*GP*A)-3')


Mass: 3069.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*TP*G)-3')


Mass: 3019.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1ERCC1/XPF/DNA complexCOMPLEXall0MULTIPLE SOURCES
2ERCC1/XPFCOMPLEX#1-#21RECOMBINANT
3DNACOMPLEX#3-#41RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Spodoptera frugiperda (fall armyworm)7108
33synthetic construct (others)32630
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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

-
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

-
Processing

EM softwareName: cryoSPARC / Version: 2 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198212 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more