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- PDB-9q25: DX2-CX3-RAD51 in the closed state -

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Basic information

Entry
Database: PDB / ID: 9q25
TitleDX2-CX3-RAD51 in the closed state
Components
  • (DNA repair protein ...) x 5
  • ssDNA (5-mer)
KeywordsDNA BINDING PROTEIN/DNA / RAD51 paralog / DX2-CX3 complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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 / crossover junction DNA endonuclease activity / mitotic recombination-dependent replication fork processing / DNA recombinase assembly / cellular response to camptothecin / 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 / t-circle formation / regulation of centrosome duplication / mitotic recombination / cellular response to hydroxyurea / 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 / single-stranded DNA helicase activity / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / ATP-dependent DNA damage sensor activity / regulation of double-strand break repair via homologous recombination / nuclear chromosome / Impaired BRCA2 binding to RAD51 / Transcriptional Regulation by E2F6 / microtubule organizing center / replication fork processing / male meiosis I / Presynaptic phase of homologous DNA pairing and strand exchange / positive regulation of G2/M transition of mitotic cell cycle / 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 / cellular response to ionizing radiation / response to gamma radiation / male germ cell nucleus / meiotic cell cycle / TP53 Regulates Transcription of DNA Repair Genes / cellular response to gamma radiation / double-strand break repair via homologous recombination / PML body / HDR through Homologous Recombination (HRR) / Meiotic recombination / response to toxic substance / multicellular organism growth / 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 / intracellular membrane-bounded organelle / DNA repair / DNA damage response / chromatin binding / centrosome / chromatin / nucleolus / perinuclear region of cytoplasm / enzyme binding
Similarity search - Function
: / DNA repair protein XRCC2 / : / : / : / : / RAD51D, N-terminal domain / DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal ...: / DNA repair protein XRCC2 / : / : / : / : / RAD51D, N-terminal 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / DNA / 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: 3.24 Å
AuthorsKoo, C.W. / Ciferri, C. / Yatskevich, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Tumor suppressors BCDX2-CX3 supercomplex and DX2-CX3 complex template RAD51 filament formation
Authors: Koo, C.W. / Ciferri, C. / Yatskevich, S.
History
DepositionAug 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 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
C: DNA repair protein RAD51 homolog 3
D: DNA repair protein RAD51 homolog 4
G: DNA repair protein RAD51 homolog 1
H: ssDNA (5-mer)
R: DNA repair protein XRCC3
X: DNA repair protein XRCC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,75814
Polymers186,7926
Non-polymers1,9668
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, 5 molecules CDGRX

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


Mass: 36167.359 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
#3: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q06609
#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: Trichoplusia ni (cabbage looper) / 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: Trichoplusia ni (cabbage looper) / References: UniProt: O43543

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DNA chain , 1 types, 1 molecules H

#4: DNA chain ssDNA (5-mer)


Mass: 1476.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 8 molecules

#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestN
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: DX2-CX3-RAD51 filament / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.2
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: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 12 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2UCSF ChimeraX1.5/v9model fitting
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86917 / Symmetry type: POINT

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