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- PDB-9zzr: Cryo-EM Structure of a RAD51 filament bound by ssDNA and the XRCC... -

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Entry
Database: PDB / ID: 9zzr
TitleCryo-EM Structure of a RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 paralog complex
Components
  • (DNA repair protein ...) x 7
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
KeywordsDNA BINDING PROTEIN/DNA / Pentameric / RAD51 / XRCC3 / RAD51C / RAD51D / XRCC2 / DNA BINDING PROTEIN-DNA complex
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 / positive regulation of mitotic cell cycle spindle assembly checkpoint / crossover junction DNA endonuclease activity / mitotic recombination-dependent replication fork processing / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / cellular response to cisplatin / nuclear ubiquitin ligase complex / regulation of centrosome duplication / DNA strand invasion / t-circle formation / mitotic recombination / cellular response to hydroxyurea / cellular response to camptothecin / replication-born double-strand break repair via sister chromatid exchange / lateral element / DNA strand exchange activity / 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 / 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 / replication fork / condensed nuclear chromosome / male germ cell nucleus / cellular response to ionizing radiation / 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 / Meiotic recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / multicellular organism growth / HDR through Homologous Recombination (HRR) / 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 / mitochondrial matrix / response to xenobiotic stimulus / DNA repair / chromatin binding / DNA damage response / centrosome / chromatin / perinuclear region of cytoplasm / nucleolus
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 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: 2.95 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: Nat Struct Mol Biol / Year: 2026
Title: Structural insight into how RAD51 paralog exchange regulates RAD51 filament formation.
Authors: Yashpal Rawal / Youngho Kwon / Lijia Jia / Eliza A Ruben / Jae-Hoon Ji / Lijuan Guo / Caleb M Stratton / Digant Nayak / Miriam Tovar / Qingming Fang / Mohd Azrin Jamalruddin / Shuo Zhou / ...Authors: Yashpal Rawal / Youngho Kwon / Lijia Jia / Eliza A Ruben / Jae-Hoon Ji / Lijuan Guo / Caleb M Stratton / Digant Nayak / Miriam Tovar / Qingming Fang / Mohd Azrin Jamalruddin / Shuo Zhou / Sahiti Kuppa / Shahrez Syed / Angela M Jasper / Jeffrey N Katz / Cody M Rogers / Hardeep Kaur / Lorena Samentar / Weixing Zhao / Eloise Dray / Fang Zhang / Svetla Stoilova-McPhie / Alexander B Taylor / Sandeep Burma / Manjeet K Rao / David S Libich / Robert Hromas / Alexander V Mazin / Maria Jasin / Daohong Zhou / Kara A Bernstein / Eric C Greene / Elizabeth V Wasmuth / Patrick Sung / Shaun K Olsen /
Abstract: Homologous recombination (HR) repairs DNA double-strand breaks and stabilizes stressed replication forks, and HR deficiency promotes genome instability and cancer. HR requires assembly of RAD51 ...Homologous recombination (HR) repairs DNA double-strand breaks and stabilizes stressed replication forks, and HR deficiency promotes genome instability and cancer. HR requires assembly of RAD51 nucleoprotein filaments on single-stranded DNA (ssDNA), a process regulated by the human RAD51 paralogs RAD51C, XRCC3, RAD51D and XRCC2. Here, using cryo-electron microscopy, we find that the RAD51-XRCC3-RAD51C complex (RAD51-X3C) assembles into an octamer in which XRCC3 engages the RAD51 DNA-binding surface and RAD51 subunits adopt a misaligned configuration incompatible with filament formation. These features define an autoinhibited RAD51-X3C state that limits nonproductive RAD51 binding to double-stranded DNA or RNA-DNA hybrids while preserving RAD51 availability for ssDNA-dependent strand exchange. We further show that the RAD51D-XRCC2 paralog complex remodels RAD51-X3C into a pentameric RAD51-X3CDX2 assembly by engaging the exposed RAD51C surface and disrupting contacts that stabilize the octamer. This remodeling exposes the RAD51 DNA-binding interface, enhances RAD51-ssDNA filament assembly, and promotes strand exchange on RPA-coated ssDNA, and yields a filament-compatible paralog assembly that integrates into ssDNA-bound RAD51 filaments. Together, these findings establish paralog exchange as a mechanism that converts an autoinhibited RAD51-X3C octamer into an activated RAD51-X3CDX2 pentamer to regulate RAD51 filament formation during HR and replication fork preservation.
History
DepositionJan 7, 2026Deposition 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
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Revision 1.1Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: DNA repair protein RAD51 homolog 1
V: DNA repair protein RAD51 homolog 1
W: DNA repair protein RAD51 homolog 1
O: DNA repair protein RAD51 homolog 1
E: DNA repair protein RAD51 homolog 1
K: DNA repair protein RAD51 homolog 1
J: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
X: DNA repair protein XRCC2
D: DNA repair protein RAD51 homolog 4
C: DNA repair protein RAD51 homolog 3
B: DNA repair protein XRCC3
F: DNA repair protein RAD51 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)393,36423
Polymers387,79612
Non-polymers5,56811
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 ... , 7 types, 11 molecules RVWOEKXDCBF

#1: Protein DNA repair protein RAD51 homolog 1 / HsRAD51 / hRAD51 / RAD51 homolog A


Mass: 34464.375 Da / Num. of mol.: 2
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
#2: Protein
DNA repair protein RAD51 homolog 1 / HsRAD51 / hRAD51 / RAD51 homolog A


Mass: 34593.555 Da / Num. of mol.: 4
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
#4: Protein DNA repair protein XRCC2 / X-ray repair cross-complementing protein 2


Mass: 29832.062 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: Protein DNA repair protein RAD51 homolog 4 / R51H3 / RAD51 homolog D / RAD51-like protein 3 / TRAD


Mass: 33548.672 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
#6: Protein DNA repair protein RAD51 homolog 3 / R51H3 / RAD51 homolog C / RAD51-like protein 2


Mass: 38021.883 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
#7: 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
#8: Protein DNA repair protein RAD51 homolog 1 / HsRAD51 / hRAD51 / RAD51 homolog A


Mass: 34239.133 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

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DNA chain / Non-polymers , 2 types, 12 molecules J

#3: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 6951.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 11 / 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

ComponentName: RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 paralog complex
Type: COMPLEX / Entity ID: #3-#7, #1 / Source: MULTIPLE SOURCES
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

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 defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 73 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123502 / Symmetry type: POINT

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