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- EMDB-4866: Abeta fibril (Morphology III) -

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Basic information

Entry
Database: EMDB / ID: EMD-4866
TitleAbeta fibril (Morphology III)
Map dataAbeta fibril (Morphology III)
Sample
  • Tissue: meninges
    • Protein or peptide: Beta amyloid (1-40)
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 7.01 Å
AuthorsKollmer M / Fandrich M
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research FoundationFA456/12-1 Germany
German Research FoundationFA456/24-1 Germany
CitationJournal: Nat Commun / Year: 2019
Title: Cryo-EM structure and polymorphism of Aβ amyloid fibrils purified from Alzheimer's brain tissue.
Authors: Marius Kollmer / William Close / Leonie Funk / Jay Rasmussen / Aref Bsoul / Angelika Schierhorn / Matthias Schmidt / Christina J Sigurdson / Mathias Jucker / Marcus Fändrich /
Abstract: The formation of Aβ amyloid fibrils is a neuropathological hallmark of Alzheimer's disease and cerebral amyloid angiopathy. However, the structure of Aβ amyloid fibrils from brain tissue is poorly ...The formation of Aβ amyloid fibrils is a neuropathological hallmark of Alzheimer's disease and cerebral amyloid angiopathy. However, the structure of Aβ amyloid fibrils from brain tissue is poorly understood. Here we report the purification of Aβ amyloid fibrils from meningeal Alzheimer's brain tissue and their structural analysis with cryo-electron microscopy. We show that these fibrils are polymorphic but consist of similarly structured protofilaments. Brain derived Aβ amyloid fibrils are right-hand twisted and their peptide fold differs sharply from previously analyzed Aβ fibrils that were formed in vitro. These data underscore the importance to use patient-derived amyloid fibrils when investigating the structural basis of the disease.
History
DepositionApr 15, 2019-
Header (metadata) releaseNov 6, 2019-
Map releaseNov 6, 2019-
UpdateNov 13, 2019-
Current statusNov 13, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4866.png

Downloads & links

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Map

FileDownload / File: emd_4866.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAbeta fibril (Morphology III)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 260 pix.
= 351. Å		1.35 Å/pix.
x 260 pix.
= 351. Å		1.35 Å/pix.
x 260 pix.
= 351. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.08135706 - 0.09370629
Average (Standard dev.)0.0000837413 (±0.0029364086)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 351.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z351.000351.000351.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.0810.0940.000

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Supplemental data

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Sample components

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Entire : meninges

EntireName: meninges
Components
  • Tissue: meninges
    • Protein or peptide: Beta amyloid (1-40)

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Supramolecule #1: meninges

SupramoleculeName: meninges / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Organ: brain / Tissue: meninges

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Macromolecule #1: Beta amyloid (1-40)

MacromoleculeName: Beta amyloid (1-40) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: BRAIN / Tissue: meninges
SequenceString:
DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 294 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 1-40 / Number real images: 1188 / Average exposure time: 24.0 sec. / Average electron dose: 40.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.45 Å
Applied symmetry - Helical parameters - Δ&Phi: 0.294 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 7.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 4960
CTF correctionSoftware - Name: Gctf
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION
FSC plot (resolution estimation)

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