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- EMDB-75395: Cryo-EM structure of Rad1-Rad10 -

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Basic information

Entry
Database: EMDB / ID: EMD-75395
TitleCryo-EM structure of Rad1-Rad10
Map dataPrimary map
Sample
  • Complex: Rad1-Rad10
    • Protein or peptide: DNA repair protein RAD1
    • Protein or peptide: DNA repair protein RAD10
KeywordsDNA repair / Structure-selective endonuclease / 3'-flap endonuclease / nucleotide excision repair / DNA BINDING PROTEIN
Function / homology
Function and homology information


removal of nonhomologous ends / double-strand break repair via single-strand annealing, removal of nonhomologous ends / endonuclease complex / DNA amplification / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / meiotic mismatch repair / resolution of meiotic recombination intermediates / mitotic recombination ...removal of nonhomologous ends / double-strand break repair via single-strand annealing, removal of nonhomologous ends / endonuclease complex / DNA amplification / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / meiotic mismatch repair / resolution of meiotic recombination intermediates / mitotic recombination / Dual incision in TC-NER / DNA endonuclease activity / nucleotide-excision repair / single-stranded DNA binding / damaged DNA binding / nucleus
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 / RuvA domain 2-like / Restriction endonuclease type II-like
Similarity search - Domain/homology
DNA repair protein RAD1 / DNA repair protein RAD10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsRodriguez Gonzalez J / Guarne A
Funding support Canada, 1 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2023-04565 Canada
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Rad1-Rad10 uses different interfaces to interact with pathway-specific DNA repair factors.
Authors: Javier Rodríguez González / Olivia T Herman / Kaden E Lewis / Lindsay A Matthews / Luke D Hess / Jennifer A Surtees / Alba Guarné /
Abstract: Saccharomyces cerevisiae Rad1-Rad10 (XPF-ERCC1 in humans) is a 3'-flap endonuclease with key roles in DNA repair. Pathway-specific repair factors determine its recruitment to specific DNA substrates. ...Saccharomyces cerevisiae Rad1-Rad10 (XPF-ERCC1 in humans) is a 3'-flap endonuclease with key roles in DNA repair. Pathway-specific repair factors determine its recruitment to specific DNA substrates. Saw1 recruits it to 3' non-homologous tail recombination intermediates, while Rad14 recruits it to UV-lesions repaired by nucleotide excision repair. However, the exact recruitment mechanisms are unknown. We determined the cryo-EM structure of the Rad1-Rad10-Saw1 complex at 3.7 Å resolution. The structure reveals that Saw1 wraps around the helicase-like domain of Rad1 defining an extensive interface. Point mutations on this surface disrupt the interaction and inhibit double-strand break repair without compromising nucleotide excision repair, indicating that Rad1-Rad10 uses different surfaces to interact with pathway-specific repair factors. Mutational analyses confirm that Rad14 and Saw1 bind to opposite faces of Rad1. Accordingly, defects on the Rad14-binding interface disrupt nucleotide excision repair without affecting double-strand break repair. In contrast to XPF-ERCC1, Rad1-Rad10 does not adopt an auto-inhibited conformation in the absence of DNA indicating that substrate binding may be regulated differently across species. Collectively, our data provide structural insight into how targeting factors interact with Rad1-Rad10 to recruit it to different DNA repair intermediates.
History
DepositionFeb 2, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75395.png

Downloads & links

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Map

FileDownload / File: emd_75395.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 416 pix.
= 280.8 Å		0.68 Å/pix.
x 416 pix.
= 280.8 Å		0.68 Å/pix.
x 416 pix.
= 280.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0253
Minimum - Maximum-0.08341674 - 0.12767144
Average (Standard dev.)0.00020824312 (±0.0039913896)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 280.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_75395_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_75395_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_75395_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rad1-Rad10

EntireName: Rad1-Rad10
Components
  • Complex: Rad1-Rad10
    • Protein or peptide: DNA repair protein RAD1
    • Protein or peptide: DNA repair protein RAD10

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Supramolecule #1: Rad1-Rad10

SupramoleculeName: Rad1-Rad10 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: DNA repair protein RAD1

MacromoleculeName: DNA repair protein RAD1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 128.703289 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MSQLFYQGDS DDELQEELTR QTTQASQSSK IKNEDEPDDS NHLNEVENED SKVLDDDAVL YPLIPNEPD DIETSKPNIN DIRPVDIQLT LPLPFQQKVV ENSLITEDAL IIMGKGLGLL DIVANLLHVL ATPTSINGQL K RALVLVLN ...String:
MGSSHHHHHH SSGLVPRGSH MSQLFYQGDS DDELQEELTR QTTQASQSSK IKNEDEPDDS NHLNEVENED SKVLDDDAVL YPLIPNEPD DIETSKPNIN DIRPVDIQLT LPLPFQQKVV ENSLITEDAL IIMGKGLGLL DIVANLLHVL ATPTSINGQL K RALVLVLN AKPIDNVRIK EALEELSWFS NTGKDDDDTA VESDDELFER PFNVVTADSL SIEKRRKLYI SGGILSITSR IL IVDLLSG IVHPNRVTGM LVLNADSLRH NSNESFILEI YRSKNTWGFI KAFSEAPETF VMEFSPLRTK MKELRLKNVL LWP RFRVEV SSCLNATNKT SHNKVIEVKV SLTNSMSQIQ FGLMECLKKC IAELSRKNPE LALDWWNMEN VLDINFIRSI DSVM VPNWH RISYESKQLV KDIRFLRHLL KMLVTSDAVD FFGEIQLSLD ANKPSVSRKY SESPWLLVDE AQLVISYAKK RIFYK NEYT LEENPKWEQL IHILHDISHE RMTNHLQGPT LVACSDNLTC LELAKVLNAS NKKRGVRQVL LNKLKWYRKQ REETKK LVK EVQSQDTFPE NATLNVSSTF SKEQVTTKRR RTRGASQVAA VEKLRNAGTN VDMEVVFEDH KLSEEIKKGS GDDLDDG QE ENAANDSKIF EIQEQENEIL IDDGDAEFDN GELEYVGDLP QHITTHFNKD LWAEHCNEYE YVDRQDEILI STFKSLND N CSLQEMMPSY IIMFEPDISF IRQIEVYKAI VKDLQPKVYF MYYGESIEEQ SHLTAIKREK DAFTKLIREN ANLSHHFET NEDLSHYKNL AERKLKLSKL RKSNTRNAGG QQGFHNLTQD VVIVDTREFN ASLPGLLYRY GIRVIPCMLT VGDYVITPDI CLERKSISD LIGSLQNNRL ANQCKKMLKY YAYPTLLIEF DEGQSFSLEP FSERRNYKNK DISTVHPISS KLSQDEIQLK L AKLVLRFP TLKIIWSSSP LQTVNIILEL KLGREQPDPS NAVILGTNKV RSDFNSTAKG LKDGDNESKF KRLLNVPGVS KI DYFNLRK KIKSFNKLQK LSWNEINELI NDEDLTDRIY YFLRTEKEEQ EQESTDENLE SPGKTTDDNA LHDHHNDVPE APV

UniProtKB: DNA repair protein RAD1

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Macromolecule #2: DNA repair protein RAD10

MacromoleculeName: DNA repair protein RAD10 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.339322 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNNTDPTSFE SILAGVAKLR KEKSGADTTG SQSLEIDASK LQQQEPQTSR RINSNQVINA FNQQKPEEWT DSKATDDYNR KRPFRSTRP GKTVLVNTTQ KENPLLNHLK STNWRYVSST GINMIYYDYL VRGRSVLFLT LTYHKLYVDY ISRRMQPLSR N ENNILIFI ...String:
MNNTDPTSFE SILAGVAKLR KEKSGADTTG SQSLEIDASK LQQQEPQTSR RINSNQVINA FNQQKPEEWT DSKATDDYNR KRPFRSTRP GKTVLVNTTQ KENPLLNHLK STNWRYVSST GINMIYYDYL VRGRSVLFLT LTYHKLYVDY ISRRMQPLSR N ENNILIFI VDDNNSEDTL NDITKLCMFN GFTLLLAFNF EQAAKYIEYL NL

UniProtKB: DNA repair protein RAD10

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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

Concentration0.54 mg/mL
BufferpH: 6.8
Component:
ConcentrationFormulaName
50.0 mMC11H26N2O6Bis Tris propane pH 6.8
75.0 mMNaClSodium chloride
5.0 mMCaCl2Calcium chloride
5.0 mMC2H6OS2-mercaptoethanol
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.2 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 7236 / Average exposure time: 2.02 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.75 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 502685
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 122366
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
FSC plot (resolution estimation)

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