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- EMDB-53058: Cryo-EM structure of a DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP c... -

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Basic information

Entry
Database: EMDB / ID: EMD-53058
TitleCryo-EM structure of a DNA-bound 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: DNA excision repair protein ERCC-1
    • Protein or peptide: Protein SLX4IP
  • Protein or peptide: Structure-specific endonuclease subunit SLX4
  • Protein or peptide: DNA repair endonuclease XPF
  • DNA: DNA strand 1
  • DNA: DNA strand 2
  • Ligand: MANGANESE (II) ION
KeywordsDNA repair / endonuclease / multiprotein complex / HYDROLASE / DNA bound complex
Function / homology
Function and homology information


Slx1-Slx4 complex / positive regulation of t-circle formation / response to intra-S DNA damage checkpoint signaling / 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 / 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 / response to intra-S DNA damage checkpoint signaling / 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 / 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 / positive regulation of telomere maintenance / TFIID-class transcription factor complex binding / 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 / double-strand break repair via nonhomologous end joining / Dual Incision in GG-NER / male gonad development / 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 / regulation of autophagy / 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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFeng J / Matthews-Palmer T / 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 9, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53058.png

Downloads & links

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Map

FileDownload / File: emd_53058.map.gz / Format: CCP4 / Size: 28.7 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.)
1.14 Å/pix.
x 196 pix.
= 224.008 Å		1.14 Å/pix.
x 196 pix.
= 224.008 Å		1.14 Å/pix.
x 196 pix.
= 224.008 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1429 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.044975277 - 0.08662689
Average (Standard dev.)0.000112557755 (±0.0032875147)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 224.00839 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53058_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map from refinement.

Fileemd_53058_half_map_1.map
AnnotationUnfiltered half map from refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map from refinement.

Fileemd_53058_half_map_2.map
AnnotationUnfiltered half map from refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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: DNA excision repair protein ERCC-1
    • Protein or peptide: Protein SLX4IP
  • Protein or peptide: Structure-specific endonuclease subunit SLX4
  • Protein or peptide: DNA repair endonuclease XPF
  • DNA: DNA strand 1
  • DNA: DNA strand 2
  • Ligand: MANGANESE (II) ION

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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: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: DNA excision repair protein ERCC-1

MacromoleculeName: DNA excision repair protein ERCC-1 / type: protein_or_peptide / ID: 1 / 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

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Macromolecule #2: Protein SLX4IP

MacromoleculeName: Protein SLX4IP / type: protein_or_peptide / ID: 2 / 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

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Macromolecule #5: Structure-specific endonuclease subunit SLX4

MacromoleculeName: Structure-specific endonuclease subunit SLX4 / type: protein_or_peptide / ID: 5 / 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

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Macromolecule #6: DNA repair endonuclease XPF

MacromoleculeName: DNA repair endonuclease XPF / type: protein_or_peptide / ID: 6 / 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

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Macromolecule #3: DNA strand 1

MacromoleculeName: DNA strand 1 / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.425912 KDa
SequenceString:
(DT)(DA)(DC)(DA)(DG)(DG)(DT)(DG)(DC)(DG) (DA)(DC)(DG)(DT)(DA)(DG)(DA)(DT)(DG)(DT) (DG)(DG)(DC)(DT)(DA)(DT)(DC)(DT)(DC) (DG)(DC)(DT)(DA)(DG)(DA)(DT)(DA)(DC)(DA) (DT) (DA)(DA)(DC)(DC)(DG)(DA)(DC)(DT) (DA)(DT)

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Macromolecule #4: DNA strand 2

MacromoleculeName: DNA strand 2 / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.585017 KDa
SequenceString:
(DA)(DT)(DA)(DG)(DT)(DC)(DG)(DG)(DT)(DT) (DA)(DT)(DG)(DT)(DA)(DT)(DC)(DT)(DA)(DG) (DC)(DG)(DA)(DG)(DA)(DT)(DA)(DA)(DA) (DG)(DT)(DG)(DT)(DA)(DG)(DA)(DT)(DG)(DC) (DA) (DG)(DC)(DG)(DT)(DG)(DG)(DA)(DC) (DA)(DT)

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Macromolecule #7: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.9
Component:
ConcentrationNameFormula
20.0 mMHEPES-KOH
200.0 mMPotassium chlorideKCl
2.0 mMManganese chlorideMnCl2
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
DetailsThe sample contained a two-fold excess of DNA fork substrate over protein complex.

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
DetailsFringe-free imaging used.
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 11694 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware: (Name: cryoSPARC (ver. 4.4.1), RELION (ver. 5.0-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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0-beta) / Number images used: 55779
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 4.0-beta)

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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-9qee:
Cryo-EM structure of a DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP complex

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