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- EMDB-11327: Oligomer structure of dimeric amyloid-beta variant dimAb -

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Basic information

Entry
Database: EMDB / ID: EMD-11327
TitleOligomer structure of dimeric amyloid-beta variant dimAb
Map datadimAb oligomer
Sample
  • Complex: oligomer of dimeric amyloid-beta.
    • Protein or peptide: dimeric amyloid-beta variant dimAb
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsSchuetzmann MP / Hasecke F / Bachmann S / Zielinski M / Haensch S / Schroeder GF / Zempel H / Hoyer W
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)726368European Union
Citation
Journal: Nat Commun / Year: 2021
Title: Endo-lysosomal Aβ concentration and pH trigger formation of Aβ oligomers that potently induce Tau missorting.
Authors: Marie P Schützmann / Filip Hasecke / Sarah Bachmann / Mara Zielinski / Sebastian Hänsch / Gunnar F Schröder / Hans Zempel / Wolfgang Hoyer /
Abstract: Amyloid-β peptide (Aβ) forms metastable oligomers >50 kDa, termed AβOs, that are more effective than Aβ amyloid fibrils at triggering Alzheimer's disease-related processes such as synaptic ...Amyloid-β peptide (Aβ) forms metastable oligomers >50 kDa, termed AβOs, that are more effective than Aβ amyloid fibrils at triggering Alzheimer's disease-related processes such as synaptic dysfunction and Tau pathology, including Tau mislocalization. In neurons, Aβ accumulates in endo-lysosomal vesicles at low pH. Here, we show that the rate of AβO assembly is accelerated 8,000-fold upon pH reduction from extracellular to endo-lysosomal pH, at the expense of amyloid fibril formation. The pH-induced promotion of AβO formation and the high endo-lysosomal Aβ concentration together enable extensive AβO formation of Aβ42 under physiological conditions. Exploiting the enhanced AβO formation of the dimeric Aβ variant dimAβ we furthermore demonstrate targeting of AβOs to dendritic spines, potent induction of Tau missorting, a key factor in tauopathies, and impaired neuronal activity. The results suggest that the endosomal/lysosomal system is a major site for the assembly of pathomechanistically relevant AβOs.
#1: Journal: BioRvix / Year: 2020
Title: Endo-lysosomal Abeta concentration and pH enable formation of Abeta oligomers that potently induce Tau missorting
Authors: Schuetzmann MP / Hasecke F / Bachmann S / Zielinski M / Haensch S / Schroeder GF / Zempel H / Hoyer W
History
DepositionJul 7, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateSep 29, 2021-
Current statusSep 29, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.24
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.24
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11327.png

Downloads & links

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Map

FileDownload / File: emd_11327.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdimAb oligomer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 128 pix.
= 119.68 Å		0.94 Å/pix.
x 128 pix.
= 119.68 Å		0.94 Å/pix.
x 128 pix.
= 119.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.24 / Movie #1: 2.24
Minimum - Maximum-2.3237567 - 10.107847
Average (Standard dev.)-2.7200985e-13 (±1.0010368)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 119.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9350.9350.935
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z119.680119.680119.680
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-2.32410.108-0.000

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Supplemental data

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Half map: odd map

Fileemd_11327_half_map_1.map
Annotationodd map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: even map

Fileemd_11327_half_map_2.map
Annotationeven map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : oligomer of dimeric amyloid-beta.

EntireName: oligomer of dimeric amyloid-beta.
Components
  • Complex: oligomer of dimeric amyloid-beta.
    • Protein or peptide: dimeric amyloid-beta variant dimAb

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Supramolecule #1: oligomer of dimeric amyloid-beta.

SupramoleculeName: oligomer of dimeric amyloid-beta. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: dimeric amyloid-beta variant dimAb

MacromoleculeName: dimeric amyloid-beta variant dimAb / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDAEFRHDSG YEVHHQKLVF FAEDVGSNKG AIIGLMVGGV VGGGGSGGGG SGGGGSGGGG SDAEFRHDSG YEVHHQKLVF FAEDVGSNKG AIIGLMVGGV V

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 29.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 32211 / Details: CRYOLO was used for automated particle picking
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER / Details: random density
Final reconstructionResolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.5) / Number images used: 10670
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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