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- PDB-9omz: Cryo-EM structure of a pentameric RAD51-XRCC3-RAD51C-RAD51D-XRCC2... -

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Basic information

Entry
Database: PDB / ID: 9omz
TitleCryo-EM structure of a pentameric RAD51-XRCC3-RAD51C-RAD51D-XRCC2 (51-X3CDX2) complex.
Components(DNA repair protein ...) x 5
KeywordsDNA BINDING PROTEIN / Pentameric / RAD51 / 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 / presynaptic intermediate filament cytoskeleton / response to glucoside ...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 / presynaptic intermediate filament cytoskeleton / response to glucoside / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic recombination-dependent replication fork processing / crossover junction DNA endonuclease activity / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / cellular response to cisplatin / DNA strand invasion / regulation of centrosome duplication / t-circle formation / cellular response to hydroxyurea / mitotic recombination / cellular response to camptothecin / replication-born double-strand break repair via sister chromatid exchange / lateral element / regulation of DNA damage checkpoint / DNA strand exchange activity / Impaired BRCA2 binding to PALB2 / gamma-tubulin binding / telomere maintenance via recombination / regulation of fibroblast apoptotic process / reciprocal meiotic recombination / single-stranded DNA helicase activity / 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) / HDR through Single Strand Annealing (SSA) / ATP-dependent DNA damage sensor activity / Resolution of D-loop Structures through Holliday Junction Intermediates / regulation of double-strand break repair via homologous recombination / nuclear chromosome / Impaired BRCA2 binding to RAD51 / Transcriptional Regulation by E2F6 / replication fork processing / 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 / condensed chromosome / DNA polymerase binding / neurogenesis / telomere maintenance / replication fork / condensed nuclear chromosome / cellular response to ionizing radiation / male germ cell nucleus / response to gamma radiation / meiotic cell cycle / TP53 Regulates Transcription of DNA Repair Genes / cellular response to gamma radiation / protein-DNA complex / PML body / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / Meiotic recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / multicellular organism growth / response to toxic substance / cell junction / 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 / spermatogenesis / in utero embryonic development / negative regulation of neuron apoptotic process / chromosome, telomeric region / regulation of cell cycle / response to xenobiotic stimulus / mitochondrial matrix / DNA repair / DNA damage response / chromatin binding / centrosome / chromatin / nucleolus / perinuclear region of 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 / Helix-hairpin-helix domain / 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 / DNA repair protein RAD51 homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.51 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 pentameric RAD51-XRCC3-RAD51C-RAD51D-XRCC2 (51-X3CDX2) 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

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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
B: DNA repair protein RAD51 homolog 1
X: DNA repair protein XRCC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,2589
Polymers184,2335
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

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DNA repair protein ... , 5 types, 5 molecules ACDBX

#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 RAD51 homolog 1 / HsRAD51 / hRAD51 / RAD51 homolog A


Mass: 37009.125 Da / Num. of mol.: 1
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
#5: 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

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Non-polymers , 1 types, 4 molecules

#6: 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

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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

Component
IDNameTypeEntity IDParent-IDSource
1Pentameric RAD51-XRCC3-RAD51C-RAD51D-XRCC2 complexCOMPLEX#1-#50MULTIPLE SOURCES
2DNA repair protein RAD51 homolog 1COMPLEX#41RECOMBINANT
3XRCC3-RAD51C-RAD51D-XRCC2COMPLEX#1-#3, #51RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Trichoplusia ni (cabbage looper)7111
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

Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.51FSC 0.143 CUT-OFF48747019OMZPOINT
23.51FSC 0.143 CUT-OFF48747019OMZPOINT
33.51FSC 0.143 CUT-OFF48747019OMZPOINT
43.51FSC 0.143 CUT-OFF48747019OMZPOINT
53.51FSC 0.143 CUT-OFF48747029OMZPOINT
63.51FSC 0.143 CUT-OFF48747029OMZPOINT
73.51FSC 0.143 CUT-OFF48747029OMZPOINT
83.51FSC 0.143 CUT-OFF48747029OMZPOINT
RefinementHighest resolution: 3.51 Å

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