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- EMDB-8834: Wild type BRCA1-BARD1 -

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Basic information

Entry
Database: EMDB / ID: 8834
TitleWild type BRCA1-BARD1
Map dataWild type BRCA1-BARD1 isolated from the human breast cancer cell line HCC70.
SampleWild type BRCA1-BARD1:
Function / homologyAnkyrin repeat region circular profile. / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Homologous DNA Pairing and Strand Exchange / BRCT domain superfamily / Nonhomologous End-Joining (NHEJ) / BRCA1-associated RING domain protein 1 / BRCA1-associated / BRCA1, serine-rich domain / Resolution of D-loop Structures through Holliday Junction Intermediates / BRCT domain ...Ankyrin repeat region circular profile. / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Homologous DNA Pairing and Strand Exchange / BRCT domain superfamily / Nonhomologous End-Joining (NHEJ) / BRCA1-associated RING domain protein 1 / BRCA1-associated / BRCA1, serine-rich domain / Resolution of D-loop Structures through Holliday Junction Intermediates / BRCT domain / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Zinc finger, C3HC4 RING-type / Zinc finger, RING-type, conserved site / Zinc finger, C3HC4 type (RING finger) / Meiotic synapsis / Metalloprotease DUBs / Zinc finger, RING/FYVE/PHD-type / Breast cancer type 1 susceptibility protein (BRCA1) / Ankyrin repeat / UCH proteinases / HDR through Homologous Recombination (HRR) / HDR through Single Strand Annealing (SSA) / SUMOylation of DNA damage response and repair proteins / Zinc finger, RING-type / Ankyrin repeat-containing domain superfamily / Ankyrin repeat-containing domain / Processing of DNA double-strand break ends / Serine-rich domain associated with BRCT / Meiotic recombination / BRCT domain profile. / Transcriptional Regulation by E2F6 / Ankyrin repeat profile. / G2/M DNA damage checkpoint / Regulation of TP53 Activity through Phosphorylation / Zinc finger RING-type signature. / TP53 Regulates Transcription of DNA Repair Genes / Presynaptic phase of homologous DNA pairing and strand exchange / Zinc finger RING-type profile. / BRCA1 C Terminus (BRCT) domain / Ankyrin repeats (3 copies) / negative regulation of mRNA 3'-end processing / positive regulation of histone H4-K16 acetylation / mitotic G2/M transition checkpoint / positive regulation of histone H4-K20 methylation / gamma-tubulin ring complex / BRCA1-BARD1 complex / BRCA1-A complex / regulation of transcription by RNA polymerase III / dosage compensation by inactivation of X chromosome / negative regulation of histone H3-K9 methylation / negative regulation of centriole replication / positive regulation of histone H3-K9 methylation / negative regulation of histone H3-K4 methylation / negative regulation of intracellular estrogen receptor signaling pathway / protein K6-linked ubiquitination / lateral element / positive regulation of histone H3-K9 acetylation / negative regulation of histone acetylation / chordate embryonic development / regulation of phosphorylation / negative regulation of fatty acid biosynthetic process / cellular response to indole-3-methanol / DNA double-strand break processing / regulation of gene expression by genetic imprinting / regulation of DNA methylation / postreplication repair / RNA polymerase binding / centrosome cycle / positive regulation of histone H3-K4 methylation / positive regulation of histone acetylation / tissue homeostasis / response to ionizing radiation / negative regulation of protein export from nucleus / negative regulation of reactive oxygen species metabolic process / signal transduction involved in G2 DNA damage checkpoint / 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 / go:0001105: / cytoplasmic ribonucleoprotein granule / ribonucleoprotein complex / positive regulation of protein ubiquitination / double-strand break repair / androgen receptor binding / androgen receptor signaling pathway / chromosome segregation / positive regulation of cell cycle arrest / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / double-strand break repair via nonhomologous end joining / double-strand break repair via homologous recombination / positive regulation of protein catabolic process / kinase binding / ec:2.3.2.27: / fatty acid biosynthetic process / chromosome / cell cycle arrest
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / 14.5 Å resolution
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
DateDeposition: Jul 17, 2017 / Header (metadata) release: Aug 9, 2017 / Map release: Oct 11, 2017 / Last update: Feb 14, 2018

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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

Downloads & links

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Map

Fileemd_8834.map.gz (map file in CCP4 format, 865 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
60 pix
4.4 Å/pix.
= 264. Å
60 pix
4.4 Å/pix.
= 264. Å
60 pix
4.4 Å/pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.4 Å
Density
Contour Level:0.622 (by author), 0.622 (movie #1):
Minimum - Maximum-0.3151399 - 0.9780071
Average (Standard dev.)0.032209106 (0.11668868)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions606060
Origin454545
Limit104104104
Spacing606060
CellA=B=C: 264 Å
α=β=γ: 90 deg.

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 / Number of components: 1
MassTheoretical: 300 kDa

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Component #1: protein, Wild type BRCA1-BARD1

ProteinName: Wild type BRCA1-BARD1 / Recombinant expression: No
MassTheoretical: 300 kDa
SourceSpecies: Homo sapiens (human)
Source (natural)Location in cell: Nucleus / Organ or tissue: Breast

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.02 mg/ml
Buffer solution: 20 mM HEPES buffer pH 7.2, 150 mM NaCl, 10 mM CaCl2, 10 mM MgCl2
pH: 7.2
Staining1% Uranyl formate
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI SPIRIT
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 68000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: -1500 - nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC
CameraDetector: FEI EAGLE (2k x 2k)

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Image acquisition

Image acquisitionNumber of digital images: 100 / Sampling size: 30 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 4008
3D reconstructionSoftware: RELION / Resolution: 14.5 Å / Resolution method: FSC 0.5 CUT-OFF / Euler angles: Empirical Bayesian approach

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