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- EMDB-75396: Cryo-EM structure of the Rad1-Rad10-Saw1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-75396
TitleCryo-EM structure of the Rad1-Rad10-Saw1 complex
Map dataPrimary map
Sample
  • Complex: Rad1-Rad10-Saw1
    • Protein or peptide: DNA repair protein RAD1
    • Protein or peptide: DNA repair protein RAD10
    • Protein or peptide: Single-strand annealing weakened protein 1
KeywordsDNA repair / structure-selective endonuclease / single-strand annealing / 3' NHTR / DNA BINDING PROTEIN
Function / homology
Function and homology information


5'-flap-structured DNA binding / removal of nonhomologous ends / double-strand break repair via single-strand annealing, removal of nonhomologous ends / endonuclease complex / DNA amplification / 3'-flap-structured DNA binding / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / meiotic mismatch repair ...5'-flap-structured DNA binding / removal of nonhomologous ends / double-strand break repair via single-strand annealing, removal of nonhomologous ends / endonuclease complex / DNA amplification / 3'-flap-structured DNA binding / 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 / Y-form DNA binding / bubble DNA binding / mitotic recombination / Dual incision in TC-NER / DNA endonuclease activity / nucleotide-excision repair / single-stranded DNA binding / damaged DNA binding / nucleus
Similarity search - Function
Single-strand annealing weakened protein 1 / Single strand annealing-weakened 1 / DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / ERCC4 domain / ERCC4 domain / ERCC4 domain ...Single-strand annealing weakened protein 1 / Single strand annealing-weakened 1 / 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 / Single-strand annealing weakened protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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_75396.png

Downloads & links

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Map

FileDownload / File: emd_75396.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 270. Å		0.68 Å/pix.
x 400 pix.
= 270. Å		0.68 Å/pix.
x 400 pix.
= 270. 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: 0.0526
Minimum - Maximum-0.13723385 - 0.3825002
Average (Standard dev.)0.00009016258 (±0.005652247)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 270.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_75396_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Locally filtered refined map

Fileemd_75396_additional_2.map
AnnotationLocally filtered refined map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_75396_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_75396_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Rad1-Rad10-Saw1

EntireName: Rad1-Rad10-Saw1
Components
  • Complex: Rad1-Rad10-Saw1
    • Protein or peptide: DNA repair protein RAD1
    • Protein or peptide: DNA repair protein RAD10
    • Protein or peptide: Single-strand annealing weakened protein 1

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Supramolecule #1: Rad1-Rad10-Saw1

SupramoleculeName: Rad1-Rad10-Saw1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 180 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: 129.80557 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKHHHHHHHG AAGTSLYKKA GENLYFQGSM SQLFYQGDSD DELQEELTRQ TTQASQSSKI KNEDEPDDSN HLNEVENEDS KVLDDDAVL YPLIPNEPDD IETSKPNIND IRPVDIQLTL PLPFQQKVVE NSLITEDALI IMGKGLGLLD IVANLLHVLA T PTSINGQL ...String:
MKHHHHHHHG AAGTSLYKKA GENLYFQGSM SQLFYQGDSD DELQEELTRQ TTQASQSSKI KNEDEPDDSN HLNEVENEDS KVLDDDAVL YPLIPNEPDD IETSKPNIND IRPVDIQLTL PLPFQQKVVE NSLITEDALI IMGKGLGLLD IVANLLHVLA T PTSINGQL KRALVLVLNA KPIDNVRIKE ALEELSWFSN TGKDDDDTAV ESDDELFERP FNVVTADSLS IEKRRKLYIS GG ILSITSR ILIVDLLSGI VHPNRVTGML VLNADSLRHN SNESFILEIY RSKNTWGFIK AFSEAPETFV MEFSPLRTKM KEL RLKNVL LWPRFRVEVS SCLNATNKTS HNKVIEVKVS LTNSMSQIQF GLMECLKKCI AELSRKNPEL ALDWWNMENV LDIN FIRSI DSVMVPNWHR ISYESKQLVK DIRFLRHLLK MLVTSDAVDF FGEIQLSLDA NKPSVSRKYS ESPWLLVDEA QLVIS YAKK RIFYKNEYTL EENPKWEQLI HILHDISHER MTNHLQGPTL VACSDNLTCL ELAKVLNASN KKRGVRQVLL NKLKWY RKQ REETKKLVKE VQSQDTFPEN ATLNVSSTFS KEQVTTKRRR TRGASQVAAV EKLRNAGTNV DMEVVFEDHK LSEEIKK GS GDDLDDGQEE NAANDSKIFE IQEQENEILI DDGDAEFDNG ELEYVGDLPQ HITTHFNKDL WAEHCNEYEY VDRQDEIL I STFKSLNDNC SLQEMMPSYI IMFEPDISFI RQIEVYKAIV KDLQPKVYFM YYGESIEEQS HLTAIKREKD AFTKLIREN ANLSHHFETN EDLSHYKNLA ERKLKLSKLR KSNTRNAGGQ QGFHNLTQDV VIVDTREFNA SLPGLLYRYG IRVIPCMLTV GDYVITPDI CLERKSISDL IGSLQNNRLA NQCKKMLKYY AYPTLLIEFD EGQSFSLEPF SERRNYKNKD ISTVHPISSK L SQDEIQLK LAKLVLRFPT LKIIWSSSPL QTVNIILELK LGREQPDPSN AVILGTNKVR SDFNSTAKGL KDGDNESKFK RL LNVPGVS KIDYFNLRKK IKSFNKLQKL SWNEINELIN DEDLTDRIYY FLRTEKEEQE QESTDENLES PGKTTDDNAL HDH HNDVPE 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: 24.614648 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSMNNTDPT SFESILAGVA KLRKEKSGAD TTGSQSLEID ASKLQQQEPQ TSRRINSNQV INAFNQQKPE EWTDSKATDD YNRKRPFRS TRPGKTVLVN TTQKENPLLN HLKSTNWRYV SSTGINMIYY DYLVRGRSVL FLTLTYHKLY VDYISRRMQP L SRNENNIL ...String:
MGSMNNTDPT SFESILAGVA KLRKEKSGAD TTGSQSLEID ASKLQQQEPQ TSRRINSNQV INAFNQQKPE EWTDSKATDD YNRKRPFRS TRPGKTVLVN TTQKENPLLN HLKSTNWRYV SSTGINMIYY DYLVRGRSVL FLTLTYHKLY VDYISRRMQP L SRNENNIL IFIVDDNNSE DTLNDITKLC MFNGFTLLLA FNFEQAAKYI EYLNL

UniProtKB: DNA repair protein RAD10

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Macromolecule #3: Single-strand annealing weakened protein 1

MacromoleculeName: Single-strand annealing weakened protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 30.08899 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSMAPSIAT VKIARDMVLP LRIFVNRKQI LQTNDKTSNK SNATIFEAPL LSNNSIICLK SPNTRIYLSQ QDKKNLCDEI KEDLLLIVY ELASPEIISS VLSKIRVGHS TDFQINVLPK LFAGADTDNA VTSHIQSVTR LAKFKYKLHY KHKWELDIFI N SIKKIANL ...String:
MGSMAPSIAT VKIARDMVLP LRIFVNRKQI LQTNDKTSNK SNATIFEAPL LSNNSIICLK SPNTRIYLSQ QDKKNLCDEI KEDLLLIVY ELASPEIISS VLSKIRVGHS TDFQINVLPK LFAGADTDNA VTSHIQSVTR LAKFKYKLHY KHKWELDIFI N SIKKIANL RHYLMFQTLT LNGFSLNAGP KTLLARKIEK QPQVPNLLIE NGDADALDTP VEEDIKPVIE FMYKPVINLG EI IDVHVLH RPRRHKVRTQ SKQPQEE

UniProtKB: Single-strand annealing weakened protein 1

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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

Concentration0.58 mg/mL
BufferpH: 6.8
Component:
ConcentrationFormulaName
50.0 mMC11H26N2O6Bis-Tris pH 6.8
50.0 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: 7776 / 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: 2.5 µm / Nominal defocus min: 1.0 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: 1085035
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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 517980
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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