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- EMDB-8834: Wild type BRCA1-BARD1 -

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Basic information

Entry
Database: EMDB / ID: EMD-8834
TitleWild type BRCA1-BARD1
Map dataWild type BRCA1-BARD1 isolated from the human breast cancer cell line HCC70.
Sample
  • Complex: Wild type BRCA1-BARD1
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 ...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 / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / DNA strand resection involved in replication fork processing / chordate embryonic development / negative regulation of fatty acid biosynthetic process / cellular response to indole-3-methanol / homologous recombination / lateral element / tissue homeostasis / XY body / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / regulation of phosphorylation / dosage compensation by inactivation of X chromosome / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to PALB2 / : / 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 / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / intracellular non-membrane-bounded organelle / response to ionizing radiation / DNA-binding transcription activator activity / 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 / protein autoubiquitination / localization / regulation of DNA repair / SUMOylation of DNA damage response and repair proteins / ubiquitin ligase complex / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of DNA repair / Meiotic synapsis / 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 / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / cytoplasmic ribonucleoprotein granule / negative regulation of cell growth / Metalloprotease DUBs / Meiotic recombination / kinase binding / ubiquitin-protein transferase activity / fatty acid biosynthetic process / positive regulation of protein catabolic process / positive regulation of angiogenesis / UCH proteinases / double-strand break repair / intrinsic apoptotic signaling pathway in response to DNA damage / KEAP1-NFE2L2 pathway / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / Neddylation / cellular response to tumor necrosis factor / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / nuclear body / protein ubiquitination / transcription cis-regulatory region binding / regulation of cell cycle / nuclear speck / ribonucleoprotein complex / positive regulation of apoptotic process / protein heterodimerization activity / DNA repair
Similarity search - Function
BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain ...BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ring finger / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Zinc finger RING-type profile. / Zinc finger, RING-type / Ankyrin repeat-containing domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Breast cancer type 1 susceptibility protein / BRCA1-associated RING domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 14.5 Å
AuthorsLiang Y / Dearnaley WJ / Kelly D
CitationJournal: 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
DepositionJul 17, 2017-
Header (metadata) releaseAug 9, 2017-
Map releaseOct 11, 2017-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.622
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.622
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8834.png

Downloads & links

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Map

FileDownload / File: emd_8834.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWild type BRCA1-BARD1 isolated from the human breast cancer cell line HCC70.
Voxel sizeX=Y=Z: 4.4 Å
Density
Contour LevelBy AUTHOR: 0.622 / Movie #1: 0.622
Minimum - Maximum-0.3151399 - 0.9780071
Average (Standard dev.)0.032209106 (±0.11668868)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin454545
Dimensions606060
Spacing606060
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.44.44.4
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS454545
NC/NR/NS606060
D min/max/mean-0.3150.9780.032

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Supplemental data

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Sample components

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Entire : Wild type BRCA1-BARD1

EntireName: Wild type BRCA1-BARD1
Components
  • Complex: Wild type BRCA1-BARD1

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Supramolecule #1: Wild type BRCA1-BARD1

SupramoleculeName: Wild type BRCA1-BARD1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.2 / Component - Name: HEPES
Details: 20 mM HEPES buffer pH 7.2, 150 mM NaCl, 10 mM CaCl2, 10 mM MgCl2
StainingType: NEGATIVE / Material: Uranyl Formate / Details: 1% Uranyl formate
GridModel: Ted Pella / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus min: -1.5 µm / Nominal magnification: 68000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingFilm 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
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5000
CTF correctionSoftware - Name: RELION (ver. 1.3b)
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.3b) / Details: Empirical Bayesian approach
Final 3D classificationNumber classes: 1 / Avg.num./class: 4008 / Software - Name: RELION (ver. 1.3b)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 1.3b) / Details: Empirical Bayesian approach
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 14.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 1.3b) / Number images used: 4008

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