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- EMDB-16434: Type Ib beta-amyloid 42 Filaments from Human Brain -

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Basic information

Entry
Database: EMDB / ID: EMD-16434
TitleType Ib beta-amyloid 42 Filaments from Human Brain
Map data
Sample
  • Tissue: beta-amyloid 42 filaments extracted from the human brain with Alzheimer's disease
    • Protein or peptide: beta-amyloid 42
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYang Y / Arseni D / Zhang W / Huang M / Lovestam SKA / Schweighauser M / Kotecha A / Murzin AG / Peak-Chew SY / Macdonald J ...Yang Y / Arseni D / Zhang W / Huang M / Lovestam SKA / Schweighauser M / Kotecha A / Murzin AG / Peak-Chew SY / Macdonald J / Lavenir I / Garringer HJ / Gelpi E / Newell KL / Kovacs GG / Vidal R / Ghetti B / Falcon B / Scheres HW / Goedert M
Funding support United Kingdom, United States, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
National Institutes of Health/National Institute on Aging (NIH/NIA) United States
CitationJournal: Science / Year: 2022
Title: Cryo-EM structures of amyloid-β 42 filaments from human brains.
Authors: Yang Yang / Diana Arseni / Wenjuan Zhang / Melissa Huang / Sofia Lövestam / Manuel Schweighauser / Abhay Kotecha / Alexey G Murzin / Sew Y Peak-Chew / Jennifer Macdonald / Isabelle Lavenir ...Authors: Yang Yang / Diana Arseni / Wenjuan Zhang / Melissa Huang / Sofia Lövestam / Manuel Schweighauser / Abhay Kotecha / Alexey G Murzin / Sew Y Peak-Chew / Jennifer Macdonald / Isabelle Lavenir / Holly J Garringer / Ellen Gelpi / Kathy L Newell / Gabor G Kovacs / Ruben Vidal / Bernardino Ghetti / Benjamin Ryskeldi-Falcon / Sjors H W Scheres / Michel Goedert /
Abstract: Filament assembly of amyloid-β peptides ending at residue 42 (Aβ42) is a central event in Alzheimer’s disease. Here, we report the cryo–electron microscopy (cryo-EM) structures of Aβ42 ...Filament assembly of amyloid-β peptides ending at residue 42 (Aβ42) is a central event in Alzheimer’s disease. Here, we report the cryo–electron microscopy (cryo-EM) structures of Aβ42 filaments from human brains. Two structurally related S-shaped protofilament folds give rise to two types of filaments. Type I filaments were found mostly in the brains of individuals with sporadic Alzheimer’s disease, and type II filaments were found in individuals with familial Alzheimer’s disease and other conditions. The structures of Aβ42 filaments from the brain differ from those of filaments assembled in vitro. By contrast, in knock-in mice, Aβ42 deposits were made of type II filaments. Knowledge of Aβ42 filament structures from human brains may lead to the development of inhibitors of assembly and improved imaging agents.
History
DepositionJan 6, 2023-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateJan 18, 2023-
Current statusJan 18, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16434.png

Downloads & links

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Map

FileDownload / File: emd_16434.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 200 pix.
= 186. Å		0.93 Å/pix.
x 200 pix.
= 186. Å		0.93 Å/pix.
x 200 pix.
= 186. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0055
Minimum - Maximum-0.02160004 - 0.029091194
Average (Standard dev.)0.00040589264 (±0.0024597887)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 186.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16434_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_16434_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : beta-amyloid 42 filaments extracted from the human brain with Alz...

EntireName: beta-amyloid 42 filaments extracted from the human brain with Alzheimer's disease
Components
  • Tissue: beta-amyloid 42 filaments extracted from the human brain with Alzheimer's disease
    • Protein or peptide: beta-amyloid 42

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Supramolecule #1: beta-amyloid 42 filaments extracted from the human brain with Alz...

SupramoleculeName: beta-amyloid 42 filaments extracted from the human brain with Alzheimer's disease
type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: beta-amyloid 42

MacromoleculeName: beta-amyloid 42 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV IA

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.4 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.2 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50990
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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