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- EMDB-70624: Cryo-EM structure of an octameric RAD51-XRCC3-RAD51C (RAD51-X3C) ... -

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Basic information

Entry
Database: EMDB / ID: EMD-70624
TitleCryo-EM structure of an octameric RAD51-XRCC3-RAD51C (RAD51-X3C) complex
Map data
Sample
  • Complex: Octameric complex RAD51-XRCC3-RAD51C
    • Complex: RAD51
      • Protein or peptide: DNA repair protein RAD51 homolog 1
    • Complex: XRCC3-RAD51C
      • Protein or peptide: DNA repair protein RAD51 homolog 3
      • Protein or peptide: DNA repair protein XRCC3
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
KeywordsOctamer / RAD51 / XRCC3 / RAD51C / DNA BINDING PROTEIN
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 / telomere maintenance via recombination / reciprocal meiotic recombination / single-stranded DNA helicase activity / 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 / 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 / interstrand cross-link repair / condensed chromosome / DNA polymerase binding / replication fork / condensed nuclear chromosome / cellular response to ionizing radiation / male germ cell nucleus / meiotic cell cycle / 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 / response to toxic substance / cell junction / single-stranded DNA binding / site of double-strand break / Factors involved in megakaryocyte development and platelet production / double-stranded DNA binding / DNA recombination / spermatogenesis / chromosome, telomeric region / response to xenobiotic stimulus / mitochondrial matrix / DNA repair / DNA damage response / chromatin binding / centrosome / chromatin / nucleolus / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / : / : / 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. ...: / : / : / 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
DNA repair protein RAD51 homolog 3 / DNA repair protein XRCC3 / DNA repair protein RAD51 homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsJia L / Ruben EA / Olsen SK / Wasmuth EV / Rawal Y / Kwon Y / Sung P
Funding support United States, 1 items
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 an octameric RAD51-XRCC3-RAD51C (RAD51-X3C) complex.
Authors: Jia L / Ruben EA / Olsen SK / Wasmuth EA / Rawal Y / Kwon Y / Sung P
History
DepositionMay 14, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70624.png

Downloads & links

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Map

FileDownload / File: emd_70624.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 320 pix.
= 278.4 Å		0.87 Å/pix.
x 320 pix.
= 278.4 Å		0.87 Å/pix.
x 320 pix.
= 278.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-1.0722055 - 1.529875
Average (Standard dev.)-0.00009131004 (±0.03135685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 278.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70624_msk_1.map
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Additional map: #1

Fileemd_70624_additional_1.map
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Half map: #2

Fileemd_70624_half_map_1.map
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Half map: #1

Fileemd_70624_half_map_2.map
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Sample components

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Entire : Octameric complex RAD51-XRCC3-RAD51C

EntireName: Octameric complex RAD51-XRCC3-RAD51C
Components
  • Complex: Octameric complex RAD51-XRCC3-RAD51C
    • Complex: RAD51
      • Protein or peptide: DNA repair protein RAD51 homolog 1
    • Complex: XRCC3-RAD51C
      • Protein or peptide: DNA repair protein RAD51 homolog 3
      • Protein or peptide: DNA repair protein XRCC3
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: Octameric complex RAD51-XRCC3-RAD51C

SupramoleculeName: Octameric complex RAD51-XRCC3-RAD51C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: RAD51

SupramoleculeName: RAD51 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: XRCC3-RAD51C

SupramoleculeName: XRCC3-RAD51C / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA repair protein RAD51 homolog 1

MacromoleculeName: DNA repair protein RAD51 homolog 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.009125 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAMQMQLEAN ADTSVEEESF GPQPISRLEQ CGINANDVKK LEEAGFHTVE AVAYAPKKEL INIKGISEAK ADKILAEAAK LVPMGFTTA TEFHQRRSEI IQITTGSKEL DKLLQGGIET GSITEMFGEF RTGKTQICHT LAVTCQLPID RGGGEGKAMY I DTEGTFRP ...String:
MAMQMQLEAN ADTSVEEESF GPQPISRLEQ CGINANDVKK LEEAGFHTVE AVAYAPKKEL INIKGISEAK ADKILAEAAK LVPMGFTTA TEFHQRRSEI IQITTGSKEL DKLLQGGIET GSITEMFGEF RTGKTQICHT LAVTCQLPID RGGGEGKAMY I DTEGTFRP ERLLAVAERY GLSGSDVLDN VAYARAFNTD HQTQLLYQAS AMMVESRYAL LIVDSATALY RTDYSGRGEL SA RQMHLAR FLRMLLRLAD EFGVAVVITN QVVAQVDGAA MFAADPKKPI GGNIIAHAST TRLYLRKGRG ETRICKIYDS PCL PEAEAM FAINADGVGD AKD

UniProtKB: DNA repair protein RAD51 homolog 1

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Macromolecule #2: DNA repair protein RAD51 homolog 3

MacromoleculeName: DNA repair protein RAD51 homolog 3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.244609 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MRGKTFRFEM QRDLVSFPLS PAVRVKLVSA GFQTAEELLE VKPSELSKEV GISKAEALET LQIIRRECLT NKPRYAGTSE SHKKCTALE LLEQEHTQGF IITFCSALDD ILGGGVPLMK TTEICGAPGV GKTQLCMQLA VDVQIPECFG GVAGEAVFID T EGSFMVDR ...String:
MRGKTFRFEM QRDLVSFPLS PAVRVKLVSA GFQTAEELLE VKPSELSKEV GISKAEALET LQIIRRECLT NKPRYAGTSE SHKKCTALE LLEQEHTQGF IITFCSALDD ILGGGVPLMK TTEICGAPGV GKTQLCMQLA VDVQIPECFG GVAGEAVFID T EGSFMVDR VVDLATACIQ HLQLIAEKHK GEEHRKALED FTLDNILSHI YYFRCRDYTE LLAQVYLLPD FLSEHSKVRL VI VDGIAFP FRHDLDDLSL RTRLLNGLAQ QMISLANNHR LAVILTNQMT TKIDRNQALL VPALGESWGH AATIRLIFHW DRK QRLATL YKSPSQKECT VLFQIKPQGF RDTVVTSACS LQTEGSLSTR KRSRDPEEEL

UniProtKB: DNA repair protein RAD51 homolog 3

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Macromolecule #3: DNA repair protein XRCC3

MacromoleculeName: DNA repair protein XRCC3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.899781 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDLDLLDLNP RIIAAIKKAK LKSVKEVLHF SGPDLKRLTN LSSPEVWHLL RTASLHLRGS SILTALQLHQ QKERFPTQHQ RLSLGCPVL DALLRGGLPL DGITELAGRS SAGKTQLALQ LCLAVQFPRQ HGGLEAGAVY ICTEDAFPHK RLQQLMAQQP R LRTDVPGE ...String:
MDLDLLDLNP RIIAAIKKAK LKSVKEVLHF SGPDLKRLTN LSSPEVWHLL RTASLHLRGS SILTALQLHQ QKERFPTQHQ RLSLGCPVL DALLRGGLPL DGITELAGRS SAGKTQLALQ LCLAVQFPRQ HGGLEAGAVY ICTEDAFPHK RLQQLMAQQP R LRTDVPGE LLQKLRFGSQ IFIEHVADVD TLLECVNKKV PVLLSRGMAR LVVIDSVAAP FRCEFDSQAS APRARHLQSL GA TLRELSS AFQSPVLCIN QVTEAMEEQG AAHGPLGFWD ERVSPALGIT WANQLLVRLL ADRLREEEAA LGCPARTLRV LSA PHLPPS SCSYTISAEG VRGTPGTQSH

UniProtKB: DNA repair protein XRCC3

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Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 6 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8faz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 165464
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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