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Yorodumi- EMDB-55292: XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filamen... -
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Open data
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Basic information
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| Title | XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on a D-loop intermediate | |||||||||||||||
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Keywords | DNA binding protein / complex / tumor suppresor | |||||||||||||||
| Function / homology | Function and homology informationtelomeric loop disassembly / double-strand break repair via synthesis-dependent strand annealing / telomere maintenance via telomere trimming / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / resolution of mitotic recombination intermediates / meiotic DNA recombinase assembly / presynaptic intermediate filament cytoskeleton / response to glucoside / crossover junction DNA endonuclease activity ...telomeric loop disassembly / double-strand break repair via synthesis-dependent strand annealing / telomere maintenance via telomere trimming / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / resolution of mitotic recombination intermediates / meiotic DNA recombinase assembly / presynaptic intermediate filament cytoskeleton / response to glucoside / crossover junction DNA endonuclease activity / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / cellular response to cisplatin / DNA recombinase assembly / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / cellular response to camptothecin / DNA strand invasion / t-circle formation / mitotic recombination / regulation of centrosome duplication / lateral element / DNA strand exchange activity / gamma-tubulin binding / Impaired BRCA2 binding to PALB2 / positive regulation of mitotic cell cycle spindle assembly checkpoint / telomere maintenance via recombination / regulation of DNA damage checkpoint / reciprocal meiotic recombination / single-stranded DNA helicase activity / centrosome cycle / sister chromatid cohesion / regulation of double-strand break repair via homologous recombination / ATP-dependent DNA damage sensor activity / 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 / microtubule organizing center / Impaired BRCA2 binding to RAD51 / nuclear replication fork / replication fork processing / positive regulation of G2/M transition of mitotic cell cycle / response to X-ray / Presynaptic phase of homologous DNA pairing and strand exchange / ATP-dependent activity, acting on DNA / interstrand cross-link repair / condensed chromosome / DNA polymerase binding / supramolecular fiber organization / telomere maintenance / cellular response to ionizing radiation / condensed nuclear chromosome / replication fork / TP53 Regulates Transcription of DNA Repair Genes / cellular response to gamma radiation / meiotic cell cycle / protein-DNA complex / PML body / double-strand break repair via homologous recombination / Meiotic recombination / response to toxic substance / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / HDR through Homologous Recombination (HRR) / 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 / chromosome, telomeric region / response to xenobiotic stimulus / mitochondrial matrix / hydrolase activity / DNA repair / centrosome / chromatin binding / DNA damage response / nucleolus / chromatin / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
| Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||||||||
Authors | Greenhough LA / West SC | |||||||||||||||
| Funding support | United Kingdom, 4 items
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Citation | Journal: Science / Year: 2026Title: Cryo-electron microscopic visualization of RAD51 filament assembly and end-capping by XRCC3-RAD51C-RAD51D-XRCC2. Authors: Luke A Greenhough / Lorenzo Galanti / Chih-Chao Liang / Simon J Boulton / Stephen C West / ![]() Abstract: Homologous recombination repairs DNA double-strand breaks and protects stalled replication forks, but how the five RAD51 paralogs contribute to these processes remains unclear. Mutations in the RAD51 ...Homologous recombination repairs DNA double-strand breaks and protects stalled replication forks, but how the five RAD51 paralogs contribute to these processes remains unclear. Mutations in the RAD51 paralogs are linked to heritable breast and ovarian cancers and the cancer-prone disease Fanconi anemia. In this work, we show that the RAD51 paralogs assemble into two distinct heterotetrameric complexes, RAD51B-RAD51C-RAD51D-XRCC2 (RAD51B complex) and XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex). The RAD51B complex promotes dynamic adenosine triphosphate hydrolysis-dependent assembly of RAD51 filaments, whereas the XRCC3 complex stably caps the 5' termini of RAD51 filaments to promote homologous pairing, as visualized by cryo-electron microscopy. Highly conserved across evolution, the XRCC3 complex reveals insights into RAD51 filament formation and capping during DNA repair and replication fork stabilization. | |||||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_55292.map.gz | 157.7 MB | EMDB map data format | |
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| Header (meta data) | emd-55292-v30.xml emd-55292.xml | 31.7 KB 31.7 KB | Display Display | EMDB header |
| Images | emd_55292.png | 48.3 KB | ||
| Filedesc metadata | emd-55292.cif.gz | 8.3 KB | ||
| Others | emd_55292_additional_1.map.gz emd_55292_half_map_1.map.gz emd_55292_half_map_2.map.gz | 149.6 MB 165.3 MB 165.3 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-55292 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-55292 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9sw0MC ![]() 9svxC ![]() 9svyC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_55292.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.95 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: #1
| File | emd_55292_additional_1.map | ||||||||||||
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-Half map: #2
| File | emd_55292_half_map_1.map | ||||||||||||
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-Half map: #1
| File | emd_55292_half_map_2.map | ||||||||||||
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Sample components
+Entire : XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filamen...
+Supramolecule #1: XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filamen...
+Macromolecule #1: DNA repair protein RAD51 homolog 4
+Macromolecule #2: DNA repair protein RAD51 homolog 1
+Macromolecule #6: DNA repair protein XRCC2
+Macromolecule #7: DNA repair protein RAD51 homolog 3
+Macromolecule #8: DNA repair protein XRCC3
+Macromolecule #3: Invading strand DNA (isDNA)
+Macromolecule #4: Complementary strand DNA (csDNA)
+Macromolecule #5: Exchanged strand DNA (esDNA)
+Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #10: CALCIUM ION
+Macromolecule #11: MAGNESIUM ION
+Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 Component:
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 | |||||||||||||||||||||
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| Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 48.4 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
United Kingdom, 4 items
Citation



















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Y (Row.)
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Processing
FIELD EMISSION GUN
