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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
MethodNegative stain / single particle reconstruction / 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
Abstract: Protein misfolding and aggregation is increasingly being recognized as a cause of disease. In Alzheimer's disease the amyloid-β peptide (Aβ) misfolds into neurotoxic oligomers and assembles into ...Protein misfolding and aggregation is increasingly being recognized as a cause of disease. In Alzheimer's disease the amyloid-β peptide (Aβ) misfolds into neurotoxic oligomers and assembles into amyloid fibrils. The Bri2 protein associated with Familial British and Danish dementias contains a BRICHOS domain, which reduces Aβ fibrillization as well as neurotoxicity in vitro and in a Drosophila model, but also rescues proteins from irreversible non-fibrillar aggregation. How these different activities are mediated is not known. Here we show that Bri2 BRICHOS monomers potently prevent neuronal network toxicity of Aβ, while dimers strongly suppress Aβ fibril formation. The dimers assemble into high-molecular-weight oligomers with an apparent two-fold symmetry, which are efficient inhibitors of non-fibrillar protein aggregation. These results indicate that Bri2 BRICHOS affects qualitatively different aspects of protein misfolding and toxicity via different quaternary structures, suggesting a means to generate molecular chaperone diversity.
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
3D viewer
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 package.

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 / / bacteria / / 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 stain
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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