+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28961 | ||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of the human BCDX2 complex | ||||||||||||||||||||||||||||||
Map data | EM map, MRC format. | ||||||||||||||||||||||||||||||
Sample |
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Keywords | DNA binding protein / ATP binding domain / homologous recombination / RAD51 paralog / RECOMBINATION | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information meiotic DNA recombinase assembly / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / female meiosis sister chromatid cohesion / blastocyst growth / crossover junction DNA endonuclease activity / somite development / telomere maintenance via recombination / Impaired BRCA2 binding to PALB2 / DNA strand invasion ...meiotic DNA recombinase assembly / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / female meiosis sister chromatid cohesion / blastocyst growth / crossover junction DNA endonuclease activity / somite development / telomere maintenance via recombination / Impaired BRCA2 binding to PALB2 / DNA strand invasion / gamma-tubulin binding / reciprocal meiotic recombination / sister chromatid cohesion / regulation of fibroblast apoptotic process / centrosome cycle / 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 / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / positive regulation of neurogenesis / ATP-dependent DNA damage sensor activity / male meiosis I / Presynaptic phase of homologous DNA pairing and strand exchange / response to X-ray / ATP-dependent activity, acting on DNA / somitogenesis / interstrand cross-link repair / four-way junction DNA binding / positive regulation of G2/M transition of mitotic cell cycle / telomere maintenance / neurogenesis / meiotic cell cycle / replication fork / response to gamma radiation / TP53 Regulates Transcription of DNA Repair Genes / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / multicellular organism growth / Meiotic recombination / cell junction / mitotic cell cycle / single-stranded DNA binding / Factors involved in megakaryocyte development and platelet production / spermatogenesis / double-stranded DNA binding / DNA recombination / in utero embryonic development / negative regulation of neuron apoptotic process / chromosome, telomeric region / regulation of cell cycle / intracellular membrane-bounded organelle / DNA repair / centrosome / positive regulation of cell population proliferation / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | ||||||||||||||||||||||||||||||
Authors | Jia L / Wasmuth EV / Ruben EA / Sung P / Rawal Y / Greene EC / Meir A / Olsen SK | ||||||||||||||||||||||||||||||
Funding support | United States, 9 items
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Citation | Journal: Nature / Year: 2023 Title: Structural insights into BCDX2 complex function in homologous recombination. Authors: Yashpal Rawal / Lijia Jia / Aviv Meir / Shuo Zhou / Hardeep Kaur / Eliza A Ruben / Youngho Kwon / Kara A Bernstein / Maria Jasin / Alexander B Taylor / Sandeep Burma / Robert Hromas / ...Authors: Yashpal Rawal / Lijia Jia / Aviv Meir / Shuo Zhou / Hardeep Kaur / Eliza A Ruben / Youngho Kwon / Kara A Bernstein / Maria Jasin / Alexander B Taylor / Sandeep Burma / Robert Hromas / Alexander V Mazin / Weixing Zhao / Daohong Zhou / Elizabeth V Wasmuth / Eric C Greene / Patrick Sung / Shaun K Olsen / Abstract: Homologous recombination (HR) fulfils a pivotal role in the repair of DNA double-strand breaks and collapsed replication forks. HR depends on the products of several paralogues of RAD51, including ...Homologous recombination (HR) fulfils a pivotal role in the repair of DNA double-strand breaks and collapsed replication forks. HR depends on the products of several paralogues of RAD51, including the tetrameric complex of RAD51B, RAD51C, RAD51D and XRCC2 (BCDX2). BCDX2 functions as a mediator of nucleoprotein filament assembly by RAD51 and single-stranded DNA (ssDNA) during HR, but its mechanism remains undefined. Here we report cryogenic electron microscopy reconstructions of human BCDX2 in apo and ssDNA-bound states. The structures reveal how the amino-terminal domains of RAD51B, RAD51C and RAD51D participate in inter-subunit interactions that underpin complex formation and ssDNA-binding specificity. Single-molecule DNA curtain analysis yields insights into how BCDX2 enhances RAD51-ssDNA nucleoprotein filament assembly. Moreover, our cryogenic electron microscopy and functional analyses explain how RAD51C alterations found in patients with cancer inactivate DNA binding and the HR mediator activity of BCDX2. Our findings shed light on the role of BCDX2 in HR and provide a foundation for understanding how pathogenic alterations in BCDX2 impact genome repair. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28961.map.gz | 32.4 MB | EMDB map data format | |
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Header (meta data) | emd-28961-v30.xml emd-28961.xml | 22 KB 22 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28961_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_28961.png | 150.3 KB | ||
Masks | emd_28961_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-28961.cif.gz | 6.7 KB | ||
Others | emd_28961_half_map_1.map.gz emd_28961_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28961 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28961 | HTTPS FTP |
-Validation report
Summary document | emd_28961_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_28961_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_28961_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | emd_28961_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28961 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28961 | HTTPS FTP |
-Related structure data
Related structure data | 8fazMC 8gbjC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28961.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | EM map, MRC format. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28961_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half Map A
File | emd_28961_half_map_1.map | ||||||||||||
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Annotation | Half Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map B
File | emd_28961_half_map_2.map | ||||||||||||
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Annotation | Half Map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of the human heterotetrameric BCDX2 complex
Entire | Name: Cryo-EM structure of the human heterotetrameric BCDX2 complex |
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Components |
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-Supramolecule #1: Cryo-EM structure of the human heterotetrameric BCDX2 complex
Supramolecule | Name: Cryo-EM structure of the human heterotetrameric BCDX2 complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: DNA repair protein RAD51 homolog 2
Macromolecule | Name: DNA repair protein RAD51 homolog 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 39.125855 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MGSKKLKRVG LSQELCDRLS RHQILTCQDF LCLSPLELMK VTGLSYRGVH ELLCMVSRAC APKMQTAYGI KAQRSADFSP AFLSTTLSA LDEALHGGVA CGSLTEITGP PGCGKTQFCI MMSILATLPT NMGGLEGAVV YIDTESAFSA ERLVEIAESR F PRYFNTEE ...String: MGSKKLKRVG LSQELCDRLS RHQILTCQDF LCLSPLELMK VTGLSYRGVH ELLCMVSRAC APKMQTAYGI KAQRSADFSP AFLSTTLSA LDEALHGGVA CGSLTEITGP PGCGKTQFCI MMSILATLPT NMGGLEGAVV YIDTESAFSA ERLVEIAESR F PRYFNTEE KLLLTSSKVH LYRELTCDEV LQRIESLEEE IISKGIKLVI LDSVASVVRK EFDAQLQGNL KERNKFLARE AS SLKYLAE EFSIPVILTN QITTHLSGAL ASQADLVSPA DDLSLSEGTS GSSCVIAALG NTWSHSVNTR LILQYLDSER RQI LIAKSP LAPFTSFVYT IKEEGLVLQA YGNSHHHHHH UniProtKB: DNA repair protein RAD51 homolog 2 |
-Macromolecule #2: DNA repair protein RAD51 homolog 3
Macromolecule | Name: DNA repair protein RAD51 homolog 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 42.244609 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 |
-Macromolecule #3: DNA repair protein RAD51 homolog 4
Macromolecule | Name: DNA repair protein RAD51 homolog 4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 35.084254 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 |
-Macromolecule #4: DNA repair protein XRCC2
Macromolecule | Name: DNA repair protein XRCC2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 32.992488 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 EFCDYKDDDD K UniProtKB: DNA repair protein XRCC2 |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #6: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Macromolecule #7: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.9 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 51.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |