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- PDB-9on2: Cryo-EM structure of a tetrameric XRCC3-RAD51C-RAD51D-XRCC2 complex -

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Basic information

Entry
Database: PDB / ID: 9on2
TitleCryo-EM structure of a tetrameric XRCC3-RAD51C-RAD51D-XRCC2 complex
Components
  • DNA repair protein RAD51 homolog 3
  • DNA repair protein RAD51 homolog 4
  • DNA repair protein XRCC2
  • DNA repair protein XRCC3
KeywordsDNA BINDING PROTEIN / Tetrameric / XRCC3 / RAD51C / RAD51D / XRCC2
Function / homology
Function and homology information


telomeric loop disassembly / meiotic DNA recombinase assembly / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / double-strand break repair via synthesis-dependent strand annealing / telomere maintenance via telomere trimming / female meiosis sister chromatid cohesion / resolution of mitotic recombination intermediates / positive regulation of mitotic cell cycle spindle assembly checkpoint / crossover junction DNA endonuclease activity ...telomeric loop disassembly / meiotic DNA recombinase assembly / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / double-strand break repair via synthesis-dependent strand annealing / telomere maintenance via telomere trimming / female meiosis sister chromatid cohesion / resolution of mitotic recombination intermediates / positive regulation of mitotic cell cycle spindle assembly checkpoint / crossover junction DNA endonuclease activity / DNA strand invasion / regulation of centrosome duplication / t-circle formation / Impaired BRCA2 binding to PALB2 / gamma-tubulin binding / telomere maintenance via recombination / regulation of fibroblast apoptotic process / reciprocal meiotic recombination / centrosome cycle / positive regulation of neurogenesis / sister chromatid cohesion / 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) / ATP-dependent DNA damage sensor activity / Resolution of D-loop Structures through Holliday Junction Intermediates / male meiosis I / microtubule organizing center / Presynaptic phase of homologous DNA pairing and strand exchange / positive regulation of G2/M transition of mitotic cell cycle / response to X-ray / ATP-dependent activity, acting on DNA / somitogenesis / interstrand cross-link repair / neurogenesis / telomere maintenance / replication fork / response to gamma radiation / meiotic cell cycle / TP53 Regulates Transcription of DNA Repair Genes / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / Meiotic recombination / multicellular organism growth / cell junction / mitotic cell cycle / single-stranded DNA binding / Factors involved in megakaryocyte development and platelet production / DNA recombination / spermatogenesis / in utero embryonic development / negative regulation of neuron apoptotic process / chromosome, telomeric region / regulation of cell cycle / DNA repair / DNA damage response / centrosome / perinuclear region of cytoplasm / mitochondrion / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / DNA repair protein XRCC2 / : / : / : / RAD51D, N-terminal domain / : / : / XRCC3/RpoA-like, helix-hairpin-helix domain / DNA recombination and repair protein, RecA-like ...: / DNA repair protein XRCC2 / : / : / : / RAD51D, N-terminal domain / : / : / XRCC3/RpoA-like, helix-hairpin-helix domain / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA repair protein RAD51 homolog 3 / DNA repair protein XRCC3 / DNA repair protein XRCC2 / DNA repair protein RAD51 homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsRuben, E.A. / Jia, L. / Olsen, S.K. / Wasmuth, E.V. / Rawal, Y. / Kwon, Y. / Sung, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of a tetrameric XRCC3-RAD51C-RAD51D-XRCC2 complex.
Authors: Ruben, E.A. / Jia, L. / Olsen, S.K. / Wasmuth, E.V. / Rawal, Y. / Kwon, Y. / Sung, P.
History
DepositionMay 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / 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 XRCC3
C: DNA repair protein RAD51 homolog 3
D: DNA repair protein RAD51 homolog 4
X: DNA repair protein XRCC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,2498
Polymers147,2244
Non-polymers2,0254
Water00
1


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

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Components

#1: 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: Trichoplusia ni (cabbage looper) / References: UniProt: O43542
#2: 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: Trichoplusia ni (cabbage looper) / References: UniProt: O43502
#3: 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: Trichoplusia ni (cabbage looper) / References: UniProt: O75771
#4: 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: Trichoplusia ni (cabbage looper) / References: UniProt: O43543
#5: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
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: Tetrameric XRCC3-RAD51C-RAD51D-XRCC2 complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 498106 / Symmetry type: POINT
RefinementHighest resolution: 3.16 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039470
ELECTRON MICROSCOPYf_angle_d0.50912825
ELECTRON MICROSCOPYf_dihedral_angle_d7.3811303
ELECTRON MICROSCOPYf_chiral_restr0.041510
ELECTRON MICROSCOPYf_plane_restr0.0041616

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