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- PDB-10qy: Cryo-EM structure of the Rad1-Rad10-Saw1 complex -

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Basic information

Entry
Database: PDB / ID: 10qy
TitleCryo-EM structure of the Rad1-Rad10-Saw1 complex
Components
  • DNA repair protein RAD1
  • DNA repair protein RAD10
  • Single-strand annealing weakened protein 1
KeywordsDNA BINDING PROTEIN / DNA repair / structure-selective endonuclease / single-strand annealing / 3' NHTR
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsRodriguez Gonzalez, J. / Guarne, A.
Funding support Canada, 1items
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, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein RAD1
B: DNA repair protein RAD10
C: Single-strand annealing weakened protein 1


Theoretical massNumber of molelcules
Total (without water)184,5093
Polymers184,5093
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein DNA repair protein RAD1


Mass: 129805.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD1, YPL022W / Production host: Escherichia coli (E. coli) / References: UniProt: P06777
#2: Protein DNA repair protein RAD10


Mass: 24614.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD10, YML095C / Production host: Escherichia coli (E. coli) / References: UniProt: P06838
#3: Protein Single-strand annealing weakened protein 1


Mass: 30088.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SAW1, YAL027W / Production host: Escherichia coli (E. coli) / References: UniProt: P39735
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rad1-Rad10-Saw1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.18 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pQLink
Buffer solutionpH: 6.8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMBis-Tris pH 6.8C11H26N2O61
250 mMSodium chlorideNaCl1
35 mMCalcium chlorideCaCl21
45 mM2-MercaptoethanolC2H6OS1
SpecimenConc.: 0.58 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.2 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 7776

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Processing

EM software
IDNameVersionCategory
1Topaz0.2.4particle selection
2SerialEMimage acquisition
4cryoSPARC4.7.0CTF correction
7ISOLDEmodel fitting
9PHENIX1.21_5207model refinement
10cryoSPARC4.7.0initial Euler assignment
11cryoSPARC4.7.0final Euler assignment
13cryoSPARC4.7.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1085035
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 517980 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 41.99 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00328719
ELECTRON MICROSCOPYf_angle_d0.563911779
ELECTRON MICROSCOPYf_chiral_restr0.04371367
ELECTRON MICROSCOPYf_plane_restr0.00461480
ELECTRON MICROSCOPYf_dihedral_angle_d5.14311136

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