+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8834 | |||||||||
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Title | Wild type BRCA1-BARD1 | |||||||||
Map data | Wild type BRCA1-BARD1 isolated from the human breast cancer cell line HCC70. | |||||||||
Sample |
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Function / homology | Function and homology information negative regulation of mRNA 3'-end processing / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / random inactivation of X chromosome / negative regulation of centriole replication / sex-chromosome dosage compensation ...negative regulation of mRNA 3'-end processing / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / 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 / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / chordate embryonic development / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / lateral element / homologous recombination / DNA strand resection involved in replication fork processing / tissue homeostasis / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / 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 / intracellular non-membrane-bounded organelle / HDR through Single Strand Annealing (SSA) / negative regulation of gene expression via chromosomal CpG island methylation / 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 / positive regulation of DNA repair / protein autoubiquitination / male germ cell nucleus / SUMOylation of DNA damage response and repair proteins / regulation of DNA repair / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ubiquitin ligase complex / Meiotic synapsis / tubulin binding / Meiotic recombination / Nonhomologous End-Joining (NHEJ) / chromosome segregation / cellular response to ionizing radiation / TP53 Regulates Transcription of DNA Repair Genes / kinase binding / G2/M DNA damage checkpoint / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / HDR through Homologous Recombination (HRR) / negative regulation of cell growth / p53 binding / Metalloprotease DUBs / fatty acid biosynthetic process / cytoplasmic ribonucleoprotein granule / positive regulation of protein catabolic process / positive regulation of angiogenesis / ubiquitin-protein transferase activity / chromosome / intrinsic apoptotic signaling pathway in response to DNA damage / UCH proteinases / KEAP1-NFE2L2 pathway / double-strand break repair / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to tumor necrosis factor / Neddylation / Regulation of TP53 Activity through Phosphorylation / transcription coactivator activity / transcription cis-regulatory region binding / damaged DNA binding / nuclear body / regulation of cell cycle / protein ubiquitination / nuclear speck / ribonucleoprotein complex / protein heterodimerization activity / positive regulation of apoptotic process / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 14.5 Å | |||||||||
Authors | Liang Y / Dearnaley WJ / Kelly D | |||||||||
Citation | Journal: Sci Adv / Year: 2017 Title: Structural analysis of BRCA1 reveals modification hotspot. Authors: Yanping Liang / William J Dearnaley / A Cameron Varano / Carly E Winton / Brian L Gilmore / Nick A Alden / Zhi Sheng / Deborah F Kelly / Abstract: Cancer cells afflicted with mutations in the breast cancer susceptibility protein (BRCA1) often suffer from increased DNA damage and genomic instability. The precise manner in which physical changes ...Cancer cells afflicted with mutations in the breast cancer susceptibility protein (BRCA1) often suffer from increased DNA damage and genomic instability. The precise manner in which physical changes to BRCA1 influence its role in DNA maintenance remains unclear. We used single-particle electron microscopy to study the three-dimensional properties of BRCA1 naturally produced in breast cancer cells. Structural studies revealed new information for full-length BRCA1, engaging its nuclear binding partner, the BRCA1-associated RING domain protein (BARD1). Equally important, we identified a region in mutated BRCA1 that was highly susceptible to ubiquitination. We refer to this site as a modification "hotspot." Ubiquitin adducts in the hotspot region proved to be biochemically reversible. Collectively, we show how key changes to BRCA1 affect its structure-function relationship, and present new insights to potentially modulate mutated BRCA1 in human cancer cells. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8834.map.gz | 527 KB | EMDB map data format | |
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Header (meta data) | emd-8834-v30.xml emd-8834.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_8834.png | 43.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8834 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8834 | HTTPS FTP |
-Validation report
Summary document | emd_8834_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_8834_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_8834_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8834 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8834 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8834.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Wild type BRCA1-BARD1 isolated from the human breast cancer cell line HCC70. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Wild type BRCA1-BARD1
Entire | Name: Wild type BRCA1-BARD1 |
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Components |
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-Supramolecule #1: Wild type BRCA1-BARD1
Supramolecule | Name: Wild type BRCA1-BARD1 / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 300 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 7.2 / Component - Name: HEPES Details: 20 mM HEPES buffer pH 7.2, 150 mM NaCl, 10 mM CaCl2, 10 mM MgCl2 |
Staining | Type: NEGATIVE / Material: Uranyl Formate / Details: 1% Uranyl formate |
Grid | Model: Ted Pella / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: FEI EAGLE (2k x 2k) / Digitization - Sampling interval: 30.0 µm / Number grids imaged: 4 / Number real images: 100 / Average electron dose: 5.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus min: -1.5 µm / Nominal magnification: 68000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |