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

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Basic information

Entry
Database: EMDB / ID: EMD-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
Sample
  • Organelle or cellular component: Oligomeric Bri2 BRICHOS
    • Protein or peptide: Bri2 BRICHOS domain
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 16.5 Å
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 ...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.
History
DepositionOct 12, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseDec 27, 2017-
UpdateOct 24, 2018-
Current statusOct 24, 2018Processing site: PDBe / Status: Released

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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

emd_3918.png

Downloads & links

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Map

FileDownload / File: emd_3918.map.gz / Format: CCP4 / Size: 4.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain 3D density map of the Bri2 Brichos domain in its oligomeric state, Molecular wieght, 370 kDaMethod: Single particle TEM
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum-0.6571486 - 2.1104124
Average (Standard dev.)0.036867473 (±0.21779104)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-52-52-52
Dimensions104104104
Spacing104104104
CellA=B=C: 215.90399 Å
α=β=γ: 90.0 °

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
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
Components
  • Organelle or cellular component: Oligomeric Bri2 BRICHOS
    • Protein or peptide: Bri2 BRICHOS domain

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Supramolecule #1: Oligomeric Bri2 BRICHOS

SupramoleculeName: Oligomeric Bri2 BRICHOS / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightExperimental: 370 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: Shuttle T7 / Recombinant plasmid: pET

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Macromolecule #1: Bri2 BRICHOS domain

MacromoleculeName: Bri2 BRICHOS domain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSQTIEENIK IFEEEEVEFS VPVPEFADDP ANIVHDFNKK LTAYLDLNLD KCYVIPLNTS IVMPPRNLLE LLINIKAGTY LPQSYLIHEH MVITDRIENI DHLGFFIYRL CHDKETYKL

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.047 mg/mL
BufferpH: 8 / Component - Concentration: 20.0 mM / Component - Formula: C2H7NO2 / Component - Name: Ammonium acetate
StainingType: NEGATIVE / Material: Uranyl Acetate / Details: 2% Uranyl Acetate
GridMaterial: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.005 kPa
DetailsPurified fraction with protein was immediately stored on ice followed by grid preparation.

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Electron microscopy

MicroscopeJEOL 2100F
Detailsper frame =1.44 e/A2
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 5120 pixel / Digitization - Dimensions - Height: 3840 pixel / Number real images: 24 / Average exposure time: 2.0 sec. / Average electron dose: 57.5 e/Å2
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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.1 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 61680 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL

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Image processing

Particle selectionNumber selected: 3000
Details: negative monitor contrast faciliated particle picking
CTF correctionSoftware - Name: EMAN2 (ver. 2.12)
Details: For low resolution data EMAN2 use a 1D structure factor during the CTF procedure
Startup modelType of model: OTHER
Details: The initial model was based on a subset of class-averages representing different views
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 16.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.12) / Number images used: 2718
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN2 (ver. 2.12)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN2 (ver. 2.12)

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