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- PDB-9svy: XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filamen... -

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Basic information

Entry
Database: PDB / ID: 9svy
TitleXRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on partially duplex DNA
Components
  • (DNA repair protein ...) x 5
  • dN-21nt
  • dN-31nt
KeywordsDNA BINDING PROTEIN / complex / tumor suppresor
Function / homology
Function and homology information


telomeric loop disassembly / double-strand break repair via synthesis-dependent strand annealing / telomere maintenance via telomere trimming / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / resolution of mitotic recombination intermediates / meiotic DNA recombinase assembly / presynaptic intermediate filament cytoskeleton / response to glucoside / crossover junction DNA endonuclease activity ...telomeric loop disassembly / double-strand break repair via synthesis-dependent strand annealing / telomere maintenance via telomere trimming / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / resolution of mitotic recombination intermediates / meiotic DNA recombinase assembly / presynaptic intermediate filament cytoskeleton / response to glucoside / crossover junction DNA endonuclease activity / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / cellular response to cisplatin / DNA recombinase assembly / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / cellular response to camptothecin / DNA strand invasion / t-circle formation / mitotic recombination / regulation of centrosome duplication / lateral element / DNA strand exchange activity / gamma-tubulin binding / Impaired BRCA2 binding to PALB2 / positive regulation of mitotic cell cycle spindle assembly checkpoint / telomere maintenance via recombination / regulation of DNA damage checkpoint / reciprocal meiotic recombination / single-stranded DNA helicase activity / centrosome cycle / sister chromatid cohesion / regulation of double-strand break repair via homologous recombination / ATP-dependent DNA damage sensor activity / HDR through Single Strand Annealing (SSA) / nuclear chromosome / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / Transcriptional Regulation by E2F6 / microtubule organizing center / Impaired BRCA2 binding to RAD51 / nuclear replication fork / replication fork processing / positive regulation of G2/M transition of mitotic cell cycle / response to X-ray / Presynaptic phase of homologous DNA pairing and strand exchange / ATP-dependent activity, acting on DNA / interstrand cross-link repair / condensed chromosome / DNA polymerase binding / supramolecular fiber organization / telomere maintenance / cellular response to ionizing radiation / condensed nuclear chromosome / replication fork / TP53 Regulates Transcription of DNA Repair Genes / cellular response to gamma radiation / meiotic cell cycle / protein-DNA complex / PML body / double-strand break repair via homologous recombination / Meiotic recombination / response to toxic substance / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / HDR through Homologous Recombination (HRR) / mitotic cell cycle / single-stranded DNA binding / site of double-strand break / Factors involved in megakaryocyte development and platelet production / double-stranded DNA binding / DNA recombination / chromosome, telomeric region / response to xenobiotic stimulus / mitochondrial matrix / hydrolase activity / DNA repair / centrosome / chromatin binding / DNA damage response / nucleolus / chromatin / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA repair protein XRCC2 / : / : / : / RAD51D, N-terminal domain / : / XRCC3/RpoA-like, helix-hairpin-helix domain / : / : / DNA recombination/repair protein Rad51 ...DNA repair protein XRCC2 / : / : / : / RAD51D, N-terminal domain / : / XRCC3/RpoA-like, helix-hairpin-helix domain / : / : / DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / : / DNA repair Rad51/transcription factor NusA, alpha-helical / SAM-like Helix-hairpin-helix tandem / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA repair protein RAD51 homolog 3 / DNA repair protein XRCC3 / DNA repair protein XRCC2 / DNA repair protein RAD51 homolog 4 / DNA repair protein RAD51 homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGreenhough, L.A. / West, S.C.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome TrustCC2098 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2098 United Kingdom
Wellcome TrustCC2098 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W01355X/1 United Kingdom
CitationJournal: Science / Year: 2026
Title: Cryo-electron microscopic visualization of RAD51 filament assembly and end-capping by XRCC3-RAD51C-RAD51D-XRCC2.
Authors: Luke A Greenhough / Lorenzo Galanti / Chih-Chao Liang / Simon J Boulton / Stephen C West /
Abstract: Homologous recombination repairs DNA double-strand breaks and protects stalled replication forks, but how the five RAD51 paralogs contribute to these processes remains unclear. Mutations in the RAD51 ...Homologous recombination repairs DNA double-strand breaks and protects stalled replication forks, but how the five RAD51 paralogs contribute to these processes remains unclear. Mutations in the RAD51 paralogs are linked to heritable breast and ovarian cancers and the cancer-prone disease Fanconi anemia. In this work, we show that the RAD51 paralogs assemble into two distinct heterotetrameric complexes, RAD51B-RAD51C-RAD51D-XRCC2 (RAD51B complex) and XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex). The RAD51B complex promotes dynamic adenosine triphosphate hydrolysis-dependent assembly of RAD51 filaments, whereas the XRCC3 complex stably caps the 5' termini of RAD51 filaments to promote homologous pairing, as visualized by cryo-electron microscopy. Highly conserved across evolution, the XRCC3 complex reveals insights into RAD51 filament formation and capping during DNA repair and replication fork stabilization.
History
DepositionOct 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA repair protein RAD51 homolog 4
M: dN-31nt
N: dN-21nt
C: DNA repair protein RAD51 homolog 3
D: DNA repair protein XRCC3
A: DNA repair protein XRCC2
E: DNA repair protein RAD51 homolog 1
F: DNA repair protein RAD51 homolog 1
G: DNA repair protein RAD51 homolog 1
H: DNA repair protein RAD51 homolog 1
I: DNA repair protein RAD51 homolog 1
J: DNA repair protein RAD51 homolog 1
K: DNA repair protein RAD51 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,57840
Polymers422,06213
Non-polymers5,51527
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA repair protein ... , 5 types, 11 molecules BCDAEFGHIJK

#1: Protein DNA repair protein RAD51 homolog 4 / R51H3 / RAD51 homolog D / RAD51-like protein 3 / TRAD


Mass: 35084.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD51D, RAD51L3 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75771
#4: Protein DNA repair protein RAD51 homolog 3 / R51H3 / RAD51 homolog C / RAD51-like protein 2


Mass: 42244.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD51C, RAD51L2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43502
#5: Protein DNA repair protein XRCC3 / X-ray repair cross-complementing protein 3


Mass: 37899.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43542
#6: Protein DNA repair protein XRCC2 / X-ray repair cross-complementing protein 2


Mass: 31995.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43543
#7: Protein
DNA repair protein RAD51 homolog 1 / HsRAD51 / hRAD51 / RAD51 homolog A


Mass: 37009.125 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD51, RAD51A, RECA / Production host: Escherichia coli (E. coli) / References: UniProt: Q06609

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DNA chain , 2 types, 2 molecules MN

#2: DNA chain dN-31nt


Mass: 9313.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain dN-21nt


Mass: 6461.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 27 molecules

#8: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#11: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on partially duplex DNA
Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Strain: Sf9
Buffer solutionpH: 7.5
Details: 25 mM HEPES-NaOH pH 7.5, 100 mM NaCl, 2.5 mM MgCl2, 2.5 mM CaCl2, 1 mM ATP, 0.25 mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESHEPES-NaOH1
2100 mMSodium chlorideNaCl1
32.5 mMMagnesium chlorideMgCl21
42.5 mMCalcium chlorideCaCl21
51 mMAdenosine triphosphateATP1
60.25 mMTris(2-carboxyethyl)phosphine hydrochlorideTCEP1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 46.3 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1Topazparticle selection
2PHENIX1.21_5207model refinement
3EPUimage acquisition
13cryoSPARC3D reconstruction3DFlex
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 24519489
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 230120 / Symmetry type: POINT
RefinementHighest resolution: 2.6 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00228231
ELECTRON MICROSCOPYf_angle_d0.4538406
ELECTRON MICROSCOPYf_dihedral_angle_d12.7764596
ELECTRON MICROSCOPYf_chiral_restr0.0394409
ELECTRON MICROSCOPYf_plane_restr0.0034759

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