[English] 日本語
- EMDB-8833: Mutated BRCA1-BARD1 -

Open data

ID or keywords:


no data

Basic information

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: Feb 14, 2018

Structure visualization

  • 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
Supplemental images

Downloads & links


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

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.4 Å
Contour Level:0.0589 (by author), 0.0589 (movie #1):
Minimum - Maximum-0.051657803 - 0.09341081
Average (Standard dev.)0.0011541239 (0.0135132745)


Space Group Number1
Map Geometry
Axis orderXYZ
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
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS454545
D min/max/mean-0.0520.0930.001

Supplemental data

Sample components

Entire Mutated BRCA1-BARD1 complex.

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

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

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

Experimental details

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

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)

Image acquisition

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

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

About Yorodumi


Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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 / EM Navigator (legacy version) / Yorodumi (legacy version)

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 / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more