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- EMDB-3918: Recombinant human Bri2 BRICHOS domain, oligomeric state -

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Basic information

Entry
Database: EMDB / ID: 3918
TitleRecombinant human Bri2 BRICHOS domain, oligomeric state
Map dataNegative stain 3D density map of the Bri2 Brichos domain in its oligomeric state, Molecular wieght, 370 kDaMethod: Single particle TEM
SampleOligomeric Bri2 BRICHOS:
Bri2 BRICHOS domain
SourceHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / 16.5 Å resolution
AuthorsHebert H / Johansson J / Nilsson HE / Koeck PJB / Chen G
CitationJournal: Nat Commun / Year: 2017
Title: Bri2 BRICHOS client specificity and chaperone activity are governed by assembly state.
Authors: Gefei Chen / Axel Abelein / Harriet E Nilsson / Axel Leppert / Yuniesky Andrade-Talavera / Simone Tambaro / Lovisa Hemmingsson / Firoz Roshan / Michael Landreh / Henrik Biverstål / Philip J B Koeck / Jenny Presto / Hans Hebert / André Fisahn / Jan Johansson
DateDeposition: Oct 12, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: Dec 27, 2017 / Last update: Dec 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3918.map.gz (map file in CCP4 format, 4500 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
104 pix
2.08 Å/pix.
= 215.904 Å
104 pix
2.08 Å/pix.
= 215.904 Å
104 pix
2.08 Å/pix.
= 215.904 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.076 Å
Density
Contour Level:1.3 (by author), 1.3 (movie #1):
Minimum - Maximum-0.6571486 - 2.1104124
Average (Standard dev.)0.036867473 (0.21779104)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions104104104
Origin-52-52-52
Limit515151
Spacing104104104
CellA=B=C: 215.90399 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.0762.0762.076
M x/y/z104104104
origin x/y/z0.0000.0000.000
length x/y/z215.904215.904215.904
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-52-52-52
NC/NR/NS104104104
D min/max/mean-0.6572.1100.037

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Supplemental data

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Sample components

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Entire Oligomeric Bri2 BRICHOS

EntireName: Oligomeric Bri2 BRICHOS / Number of components: 2
MassExperimental: 370 kDa

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Component #1: cellular-component, Oligomeric Bri2 BRICHOS

Cellular-componentName: Oligomeric Bri2 BRICHOS / Recombinant expression: No
MassExperimental: 370 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pET / Strain: Shuttle T7

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Component #2: protein, Bri2 BRICHOS domain

ProteinName: Bri2 BRICHOS domain / Recombinant expression: No
Source (engineered)Expression System: Homo sapiens (human) / Strain: Human

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.047 mg/ml / pH: 8
Staining2% Uranyl Acetate
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 2100F / Details: per frame =1.44 e/A2
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 57.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 60000 X (nominal), 61680 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: JEOL
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 24
Details: Negative stain images were collected in movie-mode at 20 frames per second. For each exposure, the comprised frames were drift corrected using the DE_process_frames-2.7.1.py script

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D2 (2*2 fold dihedral) / Number of projections: 2718
3D reconstructionAlgorithm: FOURIER SPACE / Software: EMAN2
CTF correction: For low resolution data EMAN2 use a 1D structure factor during the CTF procedure
Resolution: 16.5 Å / Resolution method: FSC 0.143 CUT-OFF

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