[English] 日本語
Yorodumi
- EMDB-53054: Cryo-EM structure of the XPF-ERCC1-XPA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53054
TitleCryo-EM structure of the XPF-ERCC1-XPA complex
Map dataPost-processed (sharpened, filtered) cryo-EM map used for model refinement.
Sample
  • Complex: XPF-ERCC1-XPA complex
    • Protein or peptide: DNA repair endonuclease XPF
    • Protein or peptide: DNA excision repair protein ERCC-1
    • Protein or peptide: DNA repair protein complementing XP-A cells
KeywordsDNA repair / endonuclease / multiprotein complex / HYDROLASE
Function / homology
Function and homology information


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 / syncytium formation / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair complex ...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 / syncytium formation / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair complex / negative regulation of telomere maintenance / single-stranded DNA endodeoxyribonuclease activity / resolution of meiotic recombination intermediates / t-circle formation / mitotic recombination / post-embryonic hemopoiesis / UV protection / 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 / replicative senescence / response to X-ray / positive regulation of transcription initiation by RNA polymerase II / protein localization to nucleus / 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 / double-strand break repair via homologous recombination / base-excision repair / double-strand break repair via nonhomologous end joining / response to toxic substance / Dual Incision in GG-NER / Formation of TC-NER Pre-Incision Complex / male gonad development / multicellular organism growth / Formation of Incision Complex in GG-NER / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / 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 / chromosome, telomeric region / cell population proliferation / regulation of autophagy / nuclear body / protein domain specific binding / DNA repair / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / XPA protein N-terminal / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site ...DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / XPA protein N-terminal / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus / XPA protein signature 1. / XPA protein signature 2. / XPA domain superfamily / ERCC4 domain / ERCC4 domain / ERCC4 domain / Putative DNA-binding domain superfamily / RuvA domain 2-like / Restriction endonuclease type II-like / Helix-hairpin-helix domain
Similarity search - Domain/homology
DNA excision repair protein ERCC-1 / DNA repair protein complementing XP-A cells / DNA repair endonuclease XPF
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFeng J / Cronin NB / Greber BJ
Funding support United Kingdom, 1 items
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 PR / Lecot M / Cronin NB / Matthews-Palmer T / Niedzwiedz W / Greber BJ
History
DepositionMar 8, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53054.png

Downloads & links

-
Map

FileDownload / File: emd_53054.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed (sharpened, filtered) cryo-EM map used for model refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 180 pix.
= 183.6 Å		1.02 Å/pix.
x 180 pix.
= 183.6 Å		1.02 Å/pix.
x 180 pix.
= 183.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0175
Minimum - Maximum-0.06414794 - 0.11354845
Average (Standard dev.)0.000026757642 (±0.0050520157)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 183.59999 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_53054_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered cryo-EM half-map.

Fileemd_53054_half_map_1.map
AnnotationUnfiltered cryo-EM half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered cryo-EM half-map.

Fileemd_53054_half_map_2.map
AnnotationUnfiltered cryo-EM half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : XPF-ERCC1-XPA complex

EntireName: XPF-ERCC1-XPA complex
Components
  • Complex: XPF-ERCC1-XPA complex
    • Protein or peptide: DNA repair endonuclease XPF
    • Protein or peptide: DNA excision repair protein ERCC-1
    • Protein or peptide: DNA repair protein complementing XP-A cells

-
Supramolecule #1: XPF-ERCC1-XPA complex

SupramoleculeName: XPF-ERCC1-XPA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 170 KDa

-
Macromolecule #1: DNA repair endonuclease XPF

MacromoleculeName: DNA repair endonuclease XPF / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 106.894539 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH ENLYFQSNAM ESGQPARRIA MAPLLEYERQ LVLELLDTDG LVVCARGLGA DRLLYHFLQL HCHPACLVLV LNTQPAEEE YFINQLKIEG VEHLPRRVTN EITSNSRYEV YTQGGVIFAT SRILVVDFLT DRIPSDLITG ILVYRAHRII E SCQEAFIL ...String:
MGSSHHHHHH ENLYFQSNAM ESGQPARRIA MAPLLEYERQ LVLELLDTDG LVVCARGLGA DRLLYHFLQL HCHPACLVLV LNTQPAEEE YFINQLKIEG VEHLPRRVTN EITSNSRYEV YTQGGVIFAT SRILVVDFLT DRIPSDLITG ILVYRAHRII E SCQEAFIL RLFRQKNKRG FIKAFTDNAV AFDTGFCHVE RVMRNLFVRK LYLWPRFHVA VNSFLEQHKP EVVEIHVSMT PT MLAIQTA ILDILNACLK ELKCHNPSLE VEDLSLENAI GKPFDKTIRH YLDPLWHQLG AKTKSLVQDL KILRTLLQYL SQY DCVTFL NLLESLRATE KAFGQNSGWL FLDSSTSMFI NARARVYHLP DAKMSKKEKI SEKMEIKEGE ETKKELVLES NPKW EALTE VLKEIEAENK ESEALGGPGQ VLICASDDRT CSQLRDYITL GAEAFLLRLY RKTFEKDSKA EEVWMKFRKE DSSKR IRKS HKRPKDPQNK ERASTKERTL KKKKRKLTLT QMVGKPEELE EEGDVEEGYR REISSSPESC PEEIKHEEFD VNLSSD AAF GILKEPLTII HPLLGCSDPY ALTRVLHEVE PRYVVLYDAE LTFVRQLEIY RASRPGKPLR VYFLIYGGST EEQRYLT AL RKEKEAFEKL IREKASMVVP EEREGRDETN LDLVRGTASA DVSTDTRKAG GQEQNGTQQS IVVDMREFRS ELPSLIHR R GIDIEPVTLE VGDYILTPEM CVERKSISDL IGSLNNGRLY SQCISMSRYY KRPVLLIEFD PSKPFSLTSR GALFQEISS NDISSKLTLL TLHFPRLRIL WCPSPHATAE LFEELKQSKP QPDAATALAI TADSETLPES EKYNPGPQDF LLKMPGVNAK NCRSLMHHV KNIAELAALS QDELTSILGN AANAKQLYDF IHTSFAEVVS KGKGKK

UniProtKB: DNA repair endonuclease XPF

-
Macromolecule #2: DNA excision repair protein ERCC-1

MacromoleculeName: DNA excision repair protein ERCC-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.598301 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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 repair protein complementing XP-A cells

MacromoleculeName: DNA repair protein complementing XP-A cells / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.422053 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAADGALPE AAALEQPAEL PASVRASIER KRQRALMLRQ ARLAARPYSA TAAAATGGMA NVKAAPKIID TGGGFILEEE EEEEQKIGK VVHQPGPVME FDYVICEECG KEFMDSYLMN HFDLPTCDNC RDADDKHKLI TKTEAKQEYL LKDCDLEKRE P PLKFIVKK ...String:
MAAADGALPE AAALEQPAEL PASVRASIER KRQRALMLRQ ARLAARPYSA TAAAATGGMA NVKAAPKIID TGGGFILEEE EEEEQKIGK VVHQPGPVME FDYVICEECG KEFMDSYLMN HFDLPTCDNC RDADDKHKLI TKTEAKQEYL LKDCDLEKRE P PLKFIVKK NPHHSQWGDM KLYLKLQIVK RSLEVWGSQE ALEEAKEVRQ ENREKMKQKK FDKKVKELRR AVRSSVWKRE TI VHQHEYG PEENLEDDMY RKTCTMCGHE LTYEKM

UniProtKB: DNA repair protein complementing XP-A cells

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.9
Component:
ConcentrationNameFormula
20.0 mMHEPES-KOH
200.0 mMPotassium chlorideKCl
2.0 mMMagnesium chlorideMgCl2
5.0 mMbeta-mercaptoethanol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 12629 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware: (Name: cryoSPARC (ver. 3.3.1), RELION (ver. 4.0-beta))
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

10337

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0-beta) / Number images used: 73737
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0-beta)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 4.0-beta)

-
Atomic model buiding 1

Initial modelPDB ID:

6sxa


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9qec:
Cryo-EM structure of the XPF-ERCC1-XPA complex

+
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://pdbjlvh1.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