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- EMDB-53054: Cryo-EM structure of the XPF-ERCC1-XPA complex -

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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 / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / 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 endonuclease activity ...positive regulation of t-circle formation / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / 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 endonuclease activity / resolution of meiotic recombination intermediates / t-circle formation / mitotic recombination / UV protection / UV-damage excision repair / negative regulation of telomere maintenance via telomere lengthening / HDR through Single Strand Annealing (SSA) / TFIID-class transcription factor complex binding / response to UV / protein localization to nucleus / telomere maintenance / nucleotide-excision repair / DNA endonuclease activity / Fanconi Anemia Pathway / promoter-specific chromatin binding / base-excision repair / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / Dual Incision in GG-NER / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / sequence-specific double-stranded DNA binding / cellular response to UV / Dual incision in TC-NER / single-stranded DNA binding / response to oxidative stress / damaged DNA binding / Hydrolases; Acting on ester bonds / nuclear body / chromosome, telomeric region / protein-macromolecule adaptor activity / protein domain specific binding / DNA repair / protein homodimerization activity / nucleoplasm / zinc ion binding / 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) / 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 / : / SAM-like Helix-hairpin-helix tandem
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: 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 8, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53054.png

Downloads & links

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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 °

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Supplemental data

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Mask #1

Fileemd_53054_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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)

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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)

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Sample components

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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

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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

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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

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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

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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

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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 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

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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

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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)

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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

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