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- EMDB-8833: Mutated BRCA1-BARD1 -

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Basic information

Entry
Database: EMDB / ID: 8833
TitleMutated BRCA1-BARD1
SampleMutated BRCA1-BARD1 complex.
SourceHomo sapiens / human
Map dataModel of BRCA1-BARD1 isolated from the mutated human breast cancer cell line HCC1937
Methodsingle particle reconstruction, at 14.7 Å resolution
AuthorsKelly DF / Dearnaley WJ
CitationSci Adv, 2017, 3, e1701386-e1701386

Sci Adv, 2017, 3, e1701386-e1701386 Yorodumi Papers
Structural analysis of BRCA1 reveals modification hotspot.
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: Oct 11, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0589
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0589
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8833.map.gz (map file in CCP4 format, 865 KB)
Projections & slices

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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)

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Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.4 Å
Density
Contour Level:0.0589 (by author), 0.0589 (movie #1):
Minimum - Maximum-0.051657803 - 0.09341081
Average (Standard dev.)0.0011541239 (0.0135132745)
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/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS454545
NC/NR/NS606060
D min/max/mean-0.0520.0930.001

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Supplemental data

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Sample components

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Entire Mutated BRCA1-BARD1 complex.

EntireName: Mutated BRCA1-BARD1 complex. / Number of components: 1

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Component #1: protein, Mutated BRCA1-BARD1 complex.

ProteinName: Mutated BRCA1-BARD1 complex. / Recombinant expression: No
SourceSpecies: Homo sapiens / human

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Experimental details

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Sample preparation

Specimen stateparticle
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: 4222
3D reconstructionSoftware: RELION / Resolution: 14.7 Å / Resolution method: FSC 0.5 CUT-OFF / Euler angles: Empirical Bayesian approach

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