|Entry||Database: EMDB / ID: 8834|
|Title||Wild type BRCA1-BARD1|
|Map data||Wild type BRCA1-BARD1 isolated from the human breast cancer cell line HCC70.|
|Sample||Wild type BRCA1-BARD1:|
|Function / homology||BRCT domain profile. / Nonhomologous End-Joining (NHEJ) / Zinc finger, C3HC4 RING-type / Homologous DNA Pairing and Strand Exchange / Zinc finger, RING-type, conserved site / Zinc finger, RING/FYVE/PHD-type / Breast cancer type 1 susceptibility protein (BRCA1) / Ankyrin repeat region circular profile. / Zinc finger, RING-type / BRCT domain ...BRCT domain profile. / Nonhomologous End-Joining (NHEJ) / Zinc finger, C3HC4 RING-type / Homologous DNA Pairing and Strand Exchange / Zinc finger, RING-type, conserved site / Zinc finger, RING/FYVE/PHD-type / Breast cancer type 1 susceptibility protein (BRCA1) / Ankyrin repeat region circular profile. / Zinc finger, RING-type / BRCT domain / Processing of DNA double-strand break ends / Resolution of D-loop Structures through Holliday Junction Intermediates / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Meiotic synapsis / SUMOylation of DNA damage response and repair proteins / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) / Metalloprotease DUBs / Ankyrin repeat-containing domain / Ankyrin repeat / BRCA1, serine-rich domain / BRCA1 C Terminus (BRCT) domain / Zinc finger RING-type profile. / Ankyrin repeat profile. / Zinc finger RING-type signature. / Meiotic recombination / Serine-rich domain associated with BRCT / Ankyrin repeats (3 copies) / BRCA1-associated / Transcriptional Regulation by E2F6 / UCH proteinases / Presynaptic phase of homologous DNA pairing and strand exchange / G2/M DNA damage checkpoint / BRCA1-associated RING domain protein 1 / Regulation of TP53 Activity through Phosphorylation / BRCT domain superfamily / Zinc finger, C3HC4 type (RING finger) / Ankyrin repeat-containing domain superfamily / TP53 Regulates Transcription of DNA Repair Genes / negative regulation of mRNA 3'-end processing / mitotic G2/M transition checkpoint / positive regulation of histone H4-K16 acetylation / positive regulation of histone H4-K20 methylation / gamma-tubulin ring complex / BRCA1-BARD1 complex / BRCA1-A complex / regulation of transcription by RNA polymerase III / negative regulation of histone H3-K9 methylation / negative regulation of centriole replication / negative regulation of histone H3-K4 methylation / positive regulation of histone H3-K9 methylation / protein K6-linked ubiquitination / negative regulation of intracellular estrogen receptor signaling pathway / dosage compensation by inactivation of X chromosome / lateral element / positive regulation of histone H3-K9 acetylation / negative regulation of histone acetylation / chordate embryonic development / cellular response to indole-3-methanol / regulation of phosphorylation / negative regulation of fatty acid biosynthetic process / DNA double-strand break processing / regulation of gene expression by genetic imprinting / regulation of DNA methylation / RNA polymerase binding / postreplication repair / centrosome cycle / positive regulation of histone H3-K4 methylation / positive regulation of histone acetylation / response to ionizing radiation / tissue homeostasis / negative regulation of reactive oxygen species metabolic process / signal transduction involved in G2 DNA damage checkpoint / negative regulation of protein export from nucleus / positive regulation of vascular endothelial growth factor production / negative regulation of G0 to G1 transition / positive regulation of DNA repair / protein autoubiquitination / ubiquitin ligase complex / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / tubulin binding / cytoplasmic ribonucleoprotein granule / positive regulation of protein ubiquitination / double-strand break repair / androgen receptor signaling pathway / androgen receptor binding / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of cell cycle arrest / chromosome segregation / ribonucleoprotein complex / double-strand break repair via homologous recombination / positive regulation of protein catabolic process / fatty acid biosynthetic process / ec:22.214.171.124: / kinase binding / double-strand break repair via nonhomologous end joining / cell cycle arrest / intrinsic apoptotic signaling pathway in response to DNA damage / chromosome|
Function and homology information
|Source||Homo sapiens (human)|
|Method||single particle reconstruction / negative staining / 14.5 Å resolution|
|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
|Date||Deposition: Jul 17, 2017 / Header (metadata) release: Aug 9, 2017 / Map release: Oct 11, 2017 / Last update: Feb 14, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_8834.map.gz (map file in CCP4 format, 865 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 4.4 Å|
CCP4 map header:
-Entire Wild type BRCA1-BARD1
|Entire||Name: Wild type BRCA1-BARD1 / Number of components: 1|
|Mass||Theoretical: 300 kDa|
-Component #1: protein, Wild type BRCA1-BARD1
|Protein||Name: Wild type BRCA1-BARD1 / Recombinant expression: No|
|Mass||Theoretical: 300 kDa|
|Source||Species: Homo sapiens (human)|
|Source (natural)||Location in cell: Nucleus / Organ or tissue: Breast|
|Specimen||Specimen state: particle / Method: negative staining|
|Sample solution||Specimen conc.: 0.02 mg/ml|
Buffer solution: 20 mM HEPES buffer pH 7.2, 150 mM NaCl, 10 mM CaCl2, 10 mM MgCl2
|Staining||1% Uranyl formate|
|Vitrification||Cryogen name: NONE|
-Electron microscopy imaging
Model: Tecnai Spirit / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI SPIRIT|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 5 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 68000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: -1500 - nm|
|Specimen Holder||Model: SIDE ENTRY, EUCENTRIC|
|Camera||Detector: FEI EAGLE (2k x 2k)|
|Image acquisition||Number of digital images: 100 / Sampling size: 30 microns|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 4008|
|3D reconstruction||Software: RELION / Resolution: 14.5 Å / Resolution method: FSC 0.5 CUT-OFF / Euler angles: Empirical Bayesian approach|
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi