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- PDB-9sw0: XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filamen... -

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Basic information

Entry
Database: PDB / ID: 9sw0
TitleXRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on a D-loop intermediate
Components
  • (DNA repair protein ...) x 5
  • Complementary strand DNA (csDNA)
  • Exchanged strand DNA (esDNA)
  • Invading strand DNA (isDNA)
KeywordsDNA BINDING PROTEIN / complex / tumor suppresor
Function / homology
Function and homology information


telomeric loop disassembly / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / meiotic DNA recombinase assembly / female meiosis sister chromatid cohesion / double-strand break repair via synthesis-dependent strand annealing / telomere maintenance via telomere trimming / resolution of mitotic recombination intermediates / presynaptic intermediate filament cytoskeleton / response to glucoside ...telomeric loop disassembly / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / meiotic DNA recombinase assembly / female meiosis sister chromatid cohesion / double-strand break repair via synthesis-dependent strand annealing / telomere maintenance via telomere trimming / resolution of mitotic recombination intermediates / presynaptic intermediate filament cytoskeleton / response to glucoside / crossover junction DNA endonuclease activity / mitotic recombination-dependent replication fork processing / DNA recombinase assembly / cellular response to cisplatin / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / regulation of centrosome duplication / DNA strand invasion / t-circle formation / mitotic recombination / cellular response to camptothecin / lateral element / DNA strand exchange activity / positive regulation of mitotic cell cycle spindle assembly checkpoint / gamma-tubulin binding / Impaired BRCA2 binding to PALB2 / regulation of DNA damage checkpoint / telomere maintenance via recombination / regulation of fibroblast apoptotic process / reciprocal meiotic recombination / single-stranded DNA helicase activity / centrosome cycle / sister chromatid cohesion / positive regulation of neurogenesis / ATP-dependent DNA damage sensor activity / regulation of double-strand break repair via homologous recombination / 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 / Impaired BRCA2 binding to RAD51 / nuclear replication fork / microtubule organizing center / male meiosis I / replication fork processing / positive regulation of G2/M transition of mitotic cell cycle / Presynaptic phase of homologous DNA pairing and strand exchange / response to X-ray / somitogenesis / ATP-dependent activity, acting on DNA / interstrand cross-link repair / condensed chromosome / DNA polymerase binding / neurogenesis / telomere maintenance / condensed nuclear chromosome / multicellular organism growth / response to gamma radiation / cellular response to ionizing radiation / replication fork / TP53 Regulates Transcription of DNA Repair Genes / meiotic cell cycle / cellular response to gamma radiation / protein-DNA complex / PML body / double-strand break repair via homologous recombination / Meiotic recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / response to toxic substance / HDR through Homologous Recombination (HRR) / cell junction / mitotic cell cycle / single-stranded DNA binding / site of double-strand break / Factors involved in megakaryocyte development and platelet production / in utero embryonic development / double-stranded DNA binding / DNA recombination / spermatogenesis / negative regulation of neuron apoptotic process / chromosome, telomeric region / regulation of cell cycle / response to xenobiotic stimulus / mitochondrial matrix / hydrolase activity / DNA repair / chromatin binding / centrosome / DNA damage response / nucleolus / chromatin / perinuclear region of cytoplasm / enzyme binding / protein-containing complex
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: 3 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
Revision 1.0Nov 12, 2025Data 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
B: DNA repair protein RAD51 homolog 4
F: DNA repair protein RAD51 homolog 1
G: DNA repair protein RAD51 homolog 1
M: Invading strand DNA (isDNA)
N: Complementary strand DNA (csDNA)
O: Exchanged strand DNA (esDNA)
E: DNA repair protein RAD51 homolog 1
A: DNA repair protein XRCC2
C: DNA repair protein RAD51 homolog 3
D: DNA repair protein XRCC3
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)456,88938
Polymers451,92914
Non-polymers4,96024
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 BFGEHIJKACD

#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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75771
#2: 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
#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 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
#8: 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

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DNA chain , 3 types, 3 molecules MNO

#3: DNA chain Invading strand DNA (isDNA)


Mass: 9460.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain Complementary strand DNA (csDNA)


Mass: 18211.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain Exchanged strand DNA (esDNA)


Mass: 17969.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 24 molecules

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


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#10: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#12: 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

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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 a D-loop intermediate
Type: COMPLEX / Entity ID: #1-#8 / 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
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: 48.4 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.21_5207model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 35223698
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29848 / Symmetry type: POINT
RefinementHighest resolution: 3 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_d0.00229161
ELECTRON MICROSCOPYf_angle_d0.45939833
ELECTRON MICROSCOPYf_dihedral_angle_d16.295050
ELECTRON MICROSCOPYf_chiral_restr0.0384570
ELECTRON MICROSCOPYf_plane_restr0.0034787

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