[English] 日本語
Yorodumi
- EMDB-53055: Cryo-EM structure of the XPF-ERCC1-SLX4(330-555)-SLX4IP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53055
TitleCryo-EM structure of the XPF-ERCC1-SLX4(330-555)-SLX4IP complex
Map dataPost-processed (sharpened, filtered) cryo-EM map.
Sample
  • Complex: XPF-ERCC1-SLX4(330-555)-SLX4IP complex
    • Protein or peptide: Protein SLX4IP
    • Protein or peptide: DNA repair endonuclease XPF
    • Protein or peptide: DNA excision repair protein ERCC-1
    • Protein or peptide: Structure-specific endonuclease subunit SLX4
KeywordsDNA repair / endonuclease / multiprotein complex / HYDROLASE
Function / homology
Function and homology information


Slx1-Slx4 complex / positive regulation of t-circle formation / DNA double-strand break processing involved in repair via single-strand annealing / pyrimidine dimer repair by nucleotide-excision repair / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / response to intra-S DNA damage checkpoint signaling / negative regulation of protection from non-homologous end joining at telomere / syncytium formation / nucleotide-excision repair factor 1 complex ...Slx1-Slx4 complex / positive regulation of t-circle formation / DNA double-strand break processing involved in repair via single-strand annealing / pyrimidine dimer repair by nucleotide-excision repair / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / response to intra-S DNA damage checkpoint signaling / 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 / negative regulation of telomere maintenance / single-stranded DNA endodeoxyribonuclease activity / resolution of meiotic recombination intermediates / telomeric D-loop disassembly / t-circle formation / mitotic recombination / post-embryonic hemopoiesis / UV protection / isotype switching / UV-damage excision repair / negative regulation of telomere maintenance via telomere lengthening / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / oogenesis / TFIID-class transcription factor complex binding / positive regulation of telomere maintenance / replicative senescence / response to X-ray / positive regulation of transcription initiation by RNA polymerase II / 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 / enzyme activator activity / double-strand break repair via homologous recombination / regulation of autophagy / double-strand break repair via nonhomologous end joining / male gonad development / Dual Incision in GG-NER / multicellular organism growth / Formation of Incision Complex in GG-NER / 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 / DNA replication / chromosome, telomeric region / cell population proliferation / DNA repair / chromatin / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Protein SLX4IP / Uncharacterized protein family UPF0492 / Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / ERCC4 domain ...Protein SLX4IP / Uncharacterized protein family UPF0492 / Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / ERCC4 domain / ERCC4 domain / ERCC4 domain / RuvA domain 2-like / Restriction endonuclease type II-like / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Helix-hairpin-helix domain / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
DNA excision repair protein ERCC-1 / Protein SLX4IP / Structure-specific endonuclease subunit SLX4 / DNA repair endonuclease XPF
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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: Nat Commun / Year: 2025
Title: Molecular basis of XPF-ERCC1 targeting to SLX4-dependent DNA repair pathways.
Authors: Junjie Feng / Peter R Martin / Szymon Kowalski / Maxime Lecot / Nora B Cronin / Teige Matthews-Palmer / Wojciech Niedzwiedz / Basil J Greber /
Abstract: The preservation and faithful propagation of genetic information is essential for all life forms and depends on cellular pathways that enable replication, recombination, and repair of DNA. The ...The preservation and faithful propagation of genetic information is essential for all life forms and depends on cellular pathways that enable replication, recombination, and repair of DNA. The multifunctional XPF-ERCC1 DNA endonuclease complex acts in several DNA repair pathways and interacts with numerous partner proteins and large DNA repair assemblies, including the nucleotide excision repair machinery and the SMX tri-endonuclease complex. Here, we report structures of XPF-ERCC1 in complex with the DNA repair factors SLX4 and SLX4IP, thereby identifying key residues responsible for direct interactions with XPF-ERCC1. When introduced into human cells, point mutations in these interfaces impair the interactions between XPF-ERCC1 and SLX4 or SLX4IP, and disruption of the XPF-SLX4IP interface leads to cis-platin sensitivity. Furthermore, our data reveal the structure of the human XPF-ERCC1-SLX4IP-SLX4 complex with DNA bound at its active site, and they complete the structural characterisation of molecular interactions required to assemble the SMX complex.
History
DepositionMar 9, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53055.png

Downloads & links

-
Map

FileDownload / File: emd_53055.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed (sharpened, filtered) cryo-EM map.
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: 0.0093
Minimum - Maximum-0.030273879 - 0.059645247
Average (Standard dev.)0.000017692095 (±0.0026323367)
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_53055_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered half-map.

Fileemd_53055_half_map_1.map
AnnotationUnfiltered half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered half-map.

Fileemd_53055_half_map_2.map
AnnotationUnfiltered half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : XPF-ERCC1-SLX4(330-555)-SLX4IP complex

EntireName: XPF-ERCC1-SLX4(330-555)-SLX4IP complex
Components
  • Complex: XPF-ERCC1-SLX4(330-555)-SLX4IP complex
    • Protein or peptide: Protein SLX4IP
    • Protein or peptide: DNA repair endonuclease XPF
    • Protein or peptide: DNA excision repair protein ERCC-1
    • Protein or peptide: Structure-specific endonuclease subunit SLX4

-
Supramolecule #1: XPF-ERCC1-SLX4(330-555)-SLX4IP complex

SupramoleculeName: XPF-ERCC1-SLX4(330-555)-SLX4IP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 210 KDa

-
Macromolecule #1: Protein SLX4IP

MacromoleculeName: Protein SLX4IP / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.62766 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASKKFAVKC GNFAVLVDLH ILPQGSNKDT SWFSEQKKEE VCLLLKETID SRVQEYLEVR KQHRPSNAEF TRSNPLSLKG YGFQITAYF LKRGIRLRCI RSTQNAELCV FPDRFVVCVS QLAFSRDLLA SQNEDLTERV LHGVSDYFAE CAESSLPPSA K LRRNALKE ...String:
MASKKFAVKC GNFAVLVDLH ILPQGSNKDT SWFSEQKKEE VCLLLKETID SRVQEYLEVR KQHRPSNAEF TRSNPLSLKG YGFQITAYF LKRGIRLRCI RSTQNAELCV FPDRFVVCVS QLAFSRDLLA SQNEDLTERV LHGVSDYFAE CAESSLPPSA K LRRNALKE IVKRTETKSS VTSKSQTRRD TVETSSDSVI AEIARRRNDG QASSSPPSES MGQAKDSIKA AESHWGLPVQ KL EKVNQTQ PEDTSGQQKP HPGERLKTGL LSRSPVCSCE SASPCPKQSP RVAKTQQKRR NCSSAEDFDH HGRVSLGSDR LVP REIIVE KSKAVRVLPA SELSDPGLLL KQDLAKTTSK EELHVLESLS SRHLMKNNPG QAQQTGLATN TERLSTIQNS PTKK RKKYE RGH

UniProtKB: Protein SLX4IP

-
Macromolecule #2: DNA repair endonuclease XPF

MacromoleculeName: DNA repair endonuclease XPF / type: protein_or_peptide / ID: 2 / 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 #3: DNA excision repair protein ERCC-1

MacromoleculeName: DNA excision repair protein ERCC-1 / type: protein_or_peptide / ID: 3 / 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 #4: Structure-specific endonuclease subunit SLX4

MacromoleculeName: Structure-specific endonuclease subunit SLX4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.617693 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASWSHPQFE KGGGSGGGSG GGSWSHPQFE KSGGGSENLY FQSNAVPQIP ECPICGKPFL TLKSRTSHLK QCAVKMEVGP QLLLQAVRL QTAQPEGSSS PPMFSFSDHS RGLKRRGPTS KKEPRKRRKV DEAPSEDLLV AMALSRSEME PGAAVPALRL E SAFSERIR ...String:
MASWSHPQFE KGGGSGGGSG GGSWSHPQFE KSGGGSENLY FQSNAVPQIP ECPICGKPFL TLKSRTSHLK QCAVKMEVGP QLLLQAVRL QTAQPEGSSS PPMFSFSDHS RGLKRRGPTS KKEPRKRRKV DEAPSEDLLV AMALSRSEME PGAAVPALRL E SAFSERIR PEAENKSRKK KPPVSPPLLL VQDSETTGRQ IEDRVALLLS EEVELSSTPP LPASRILKEG WERAGQCPPP PE RKQSFLW EGSALTGAWA MEDFYTARLV PPLV

UniProtKB: Structure-specific endonuclease subunit SLX4

-
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: 277 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: 14573 / 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) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0-beta) / Number images used: 22617
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 model
PDB IDChain

6sxa

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9qed:
Cryo-EM structure of the XPF-ERCC1-SLX4(330-555)-SLX4IP 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://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