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Yorodumi- EMDB-34212: Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34212 | |||||||||
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Title | Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | nucleosome / BRCA1/BARD1 / BRCA1 / BARD1 / H2AK127 / H2AK127-UbcH5c-Ub / NUCLEAR PROTEIN | |||||||||
Function / homology | Function and homology information Inhibition of DNA recombination at telomere / negative regulation of mRNA 3'-end processing / Deposition of new CENPA-containing nucleosomes at the centromere / DNA Damage/Telomere Stress Induced Senescence / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Condensation of Prophase Chromosomes / Metalloprotease DUBs / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function ...Inhibition of DNA recombination at telomere / negative regulation of mRNA 3'-end processing / Deposition of new CENPA-containing nucleosomes at the centromere / DNA Damage/Telomere Stress Induced Senescence / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Condensation of Prophase Chromosomes / Metalloprotease DUBs / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / HDACs deacetylate histones / BRCA1-BARD1 complex / BRCA1-C complex / PRC2 methylates histones and DNA / BRCA1-B complex / UCH proteinases / BRCA1-A complex / random inactivation of X chromosome / negative regulation of centriole replication / sex-chromosome dosage compensation / negative regulation of intracellular estrogen receptor signaling pathway / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / gamma-tubulin ring complex / RMTs methylate histone arginines / nuclear ubiquitin ligase complex / DNA strand resection involved in replication fork processing / chordate embryonic development / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / homologous recombination / lateral element / tissue homeostasis / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / Ub-specific processing proteases / regulation of phosphorylation / Impaired BRCA2 binding to PALB2 / XY body / mitotic G2/M transition checkpoint / negative regulation of protein export from nucleus / postreplication repair / DNA repair complex / RNA polymerase binding / 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 / negative regulation of gene expression via chromosomal CpG island methylation / intracellular non-membrane-bounded organelle / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA-binding transcription activator activity / response to ionizing radiation / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / localization / protein autoubiquitination / regulation of DNA repair / SUMOylation of DNA damage response and repair proteins / heterochromatin organization / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ubiquitin ligase complex / nucleosomal DNA binding / Meiotic synapsis / positive regulation of DNA repair / tubulin binding / male germ cell nucleus / chromosome segregation / cellular response to ionizing radiation / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / Metalloprotease DUBs / negative regulation of cell growth / Meiotic recombination / fatty acid biosynthetic process / kinase binding / cytoplasmic ribonucleoprotein granule / positive regulation of protein catabolic process / structural constituent of chromatin / ubiquitin-protein transferase activity / positive regulation of angiogenesis / UCH proteinases / intrinsic apoptotic signaling pathway in response to DNA damage / KEAP1-NFE2L2 pathway / nucleosome / double-strand break repair / nucleosome assembly / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.87 Å | |||||||||
Authors | Ai HS / Zebin T / Zhiheng D / Jiakun T / Liying Z / Jia-Bin L / Man P / Liu L | |||||||||
Funding support | China, 1 items
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Citation | Journal: Chem / Year: 2023 Title: Synthetic E2-Ub-nucleosome conjugates for studying nucleosome ubiquitination. Authors: Ai HS / Tong Z / Deng Z / Tian J / Zhang L / Sun M / Du Y / Xu Z / Shi Q / Liang L / Zheng Q / Li JB / Pan M / Liu L | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34212.map.gz | 59.3 MB | EMDB map data format | |
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Header (meta data) | emd-34212-v30.xml emd-34212.xml | 24.8 KB 24.8 KB | Display Display | EMDB header |
Images | emd_34212.png | 70.8 KB | ||
Masks | emd_34212_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-34212.cif.gz | 6.6 KB | ||
Others | emd_34212_additional_1.map.gz emd_34212_half_map_1.map.gz emd_34212_half_map_2.map.gz | 49.5 MB 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34212 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34212 | HTTPS FTP |
-Validation report
Summary document | emd_34212_validation.pdf.gz | 964.6 KB | Display | EMDB validaton report |
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Full document | emd_34212_full_validation.pdf.gz | 964.2 KB | Display | |
Data in XML | emd_34212_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_34212_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34212 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34212 | HTTPS FTP |
-Related structure data
Related structure data | 8grqMC 8grmC 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_34212.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.074 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34212_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_34212_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_34212_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34212_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of BRCA1/BARD1 and H2AK127-UbcH5c-Ub nucleosome
+Supramolecule #1: Complex of BRCA1/BARD1 and H2AK127-UbcH5c-Ub nucleosome
+Macromolecule #1: Histone H3
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1-H
+Macromolecule #4: H2B
+Macromolecule #7: Breast cancer type 1 susceptibility protein
+Macromolecule #8: BRCA1-associated RING domain protein 1
+Macromolecule #9: Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isofo...
+Macromolecule #5: DNA (147-MER)
+Macromolecule #6: DNA (147-MER)
+Macromolecule #10: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68006 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |