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- EMDB-55291: XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filamen... -

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Basic information

Entry
Database: EMDB / ID: EMD-55291
TitleXRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on partially duplex DNA
Map data
Sample
  • Complex: XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on partially duplex DNA
    • Protein or peptide: x 5 types
    • DNA: x 2 types
  • Ligand: x 4 types
KeywordsDNA binding protein / complex / tumor suppresor
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 / t-circle formation / 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 / regulation of centrosome duplication / cellular response to hydroxyurea / mitotic recombination / DNA strand exchange activity / replication-born double-strand break repair via sister chromatid exchange / lateral element / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / telomere maintenance via recombination / gamma-tubulin binding / regulation of fibroblast apoptotic process / single-stranded DNA helicase activity / reciprocal meiotic recombination / centrosome cycle / positive regulation of neurogenesis / 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) / sister chromatid cohesion / 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 / male meiosis I / replication fork processing / 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 / response to gamma radiation / cellular response to ionizing radiation / meiotic cell cycle / male germ cell nucleus / 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) / response to toxic substance / Meiotic recombination / 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 / spermatogenesis / DNA recombination / 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 / intracellular membrane-bounded organelle / DNA damage response / centrosome / chromatin binding / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGreenhough LA / West SC
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Wellcome TrustCC2098 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2098 United Kingdom
Wellcome TrustCC2098 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W01355X/1 United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM visualization of RAD51 filament assembly and end-capping by XRCC3-RAD51C-RAD51D-XRCC2
Authors: Greenhough LA / Galanti L / Liang CC / Boulton SJ / West SC
History
DepositionOct 3, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55291.png

Downloads & links

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Map

FileDownload / File: emd_55291.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 360 pix.
= 342. Å		0.95 Å/pix.
x 360 pix.
= 342. Å		0.95 Å/pix.
x 360 pix.
= 342. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.017712722 - 0.052124877
Average (Standard dev.)0.00006566462 (±0.0009501536)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_55291_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55291_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55291_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filamen...

EntireName: XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on partially duplex DNA
Components
  • Complex: XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on partially duplex DNA
    • Protein or peptide: DNA repair protein RAD51 homolog 4
    • DNA: dN-31nt
    • DNA: dN-21nt
    • Protein or peptide: DNA repair protein RAD51 homolog 3
    • Protein or peptide: DNA repair protein XRCC3
    • Protein or peptide: DNA repair protein XRCC2
    • Protein or peptide: DNA repair protein RAD51 homolog 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: CALCIUM ION

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Supramolecule #1: XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filamen...

SupramoleculeName: XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on partially duplex DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA repair protein RAD51 homolog 4

MacromoleculeName: DNA repair protein RAD51 homolog 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.084254 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGVLRVGLCP GLTEEMIQLL RSHRIKTVVD LVSADLEEVA QKCGLSYKAL VALRRVLLAQ FSAFPVNGAD LYEELKTSTA ILSTGIGSL DKLLDAGLYT GEVTEIVGGP GSGKTQVCLC MAANVAHGLQ QNVLYVDSNG GLTASRLLQL LQAKTQDEEE Q AEALRRIQ ...String:
MGVLRVGLCP GLTEEMIQLL RSHRIKTVVD LVSADLEEVA QKCGLSYKAL VALRRVLLAQ FSAFPVNGAD LYEELKTSTA ILSTGIGSL DKLLDAGLYT GEVTEIVGGP GSGKTQVCLC MAANVAHGLQ QNVLYVDSNG GLTASRLLQL LQAKTQDEEE Q AEALRRIQ VVHAFDIFQM LDVLQELRGT VAQQVTGSSG TVKVVVVDSV TAVVSPLLGG QQREGLALMM QLARELKTLA RD LGMAVVV TNHITRDRDS GRLKPALGRS WSFVPSTRIL LDTIEGAGAS GGRRMACLAK SSRQPTGFQE MVDIGTWGTS EQS ATLQGD QT

UniProtKB: DNA repair protein RAD51 homolog 4

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Macromolecule #4: DNA repair protein RAD51 homolog 3

MacromoleculeName: DNA repair protein RAD51 homolog 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.244609 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #5: DNA repair protein XRCC3

MacromoleculeName: DNA repair protein XRCC3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.899781 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #6: DNA repair protein XRCC2

MacromoleculeName: DNA repair protein XRCC2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.995525 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MCSAFHRAES GTELLARLEG RSSLKEIEPN LFADEDSPVH GDILEFHGPE GTGKTEMLYH LTARCILPKS EGGLEVEVLF IDTDYHFDM LRLVTILEHR LSQSSEEIIK YCLGRFFLVY CSSSTHLLLT LYSLESMFCS HPSLCLLILD SLSAFYWIDR V NGGESVNL ...String:
MCSAFHRAES GTELLARLEG RSSLKEIEPN LFADEDSPVH GDILEFHGPE GTGKTEMLYH LTARCILPKS EGGLEVEVLF IDTDYHFDM LRLVTILEHR LSQSSEEIIK YCLGRFFLVY CSSSTHLLLT LYSLESMFCS HPSLCLLILD SLSAFYWIDR V NGGESVNL QESTLRKCSQ CLEKLVNDYR LVLFATTQTI MQKASSSSEE PSHASRRLCD VDIDYRPYLC KAWQQLVKHR MF FSKQDDS QSSNQFSLVS RCLKSNSLKK HFFIIGESGV EFC

UniProtKB: DNA repair protein XRCC2

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Macromolecule #7: DNA repair protein RAD51 homolog 1

MacromoleculeName: DNA repair protein RAD51 homolog 1 / type: protein_or_peptide / ID: 7 / Number of copies: 7 / 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: dN-31nt

MacromoleculeName: dN-31nt / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.313001 KDa
SequenceString:
(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC) (DT)(DA)(DT)(DC)(DG)(DA)(DA)(DT)(DC)(DC) (DG)(DT)(DC)(DT)(DA)(DA)(DA)(DG)(DT) (DT)(DA)

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Macromolecule #3: dN-21nt

MacromoleculeName: dN-21nt / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.461208 KDa
SequenceString:
(DT)(DA)(DA)(DC)(DT)(DT)(DT)(DA)(DG)(DA) (DC)(DG)(DG)(DA)(DT)(DT)(DC)(DG)(DA)(DT) (DA)

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Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 9 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 10 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #11: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 11 / Number of copies: 7 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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
Component:
ConcentrationFormulaName
25.0 mMHEPES-NaOHHEPES
100.0 mMNaClSodium chloride
2.5 mMMgCl2Magnesium chloride
2.5 mMCaCl2Calcium chloride
1.0 mMATPAdenosine triphosphate
0.25 mMTCEPTris(2-carboxyethyl)phosphine hydrochloride

Details: 25 mM HEPES-NaOH pH 7.5, 100 mM NaCl, 2.5 mM MgCl2, 2.5 mM CaCl2, 1 mM ATP, 0.25 mM TCEP
GridModel: UltrAuFoil R2/2 / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 46.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 24519489
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER / Details: Initial model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 230120
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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