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- EMDB-12592: Amyloid-beta fibril of the Uppsala variant (polymorph 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-12592
TitleAmyloid-beta fibril of the Uppsala variant (polymorph 1)
Map dataAbeta36 - polymorph 1
Sample
  • Complex: amyloid fibril of Abeta36
    • Protein or peptide: amyloid-beta
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsSchroder GF / Zielinski M / Willbold D
CitationJournal: Sci Transl Med / Year: 2021
Title: The deletion causes early onset autosomal dominant Alzheimer's disease by altering APP processing and increasing amyloid β fibril formation.
Authors: María Pagnon de la Vega / Vilmantas Giedraitis / Wojciech Michno / Lena Kilander / Gökhan Güner / Mara Zielinski / Malin Löwenmark / RoseMarie Brundin / Torsten Danfors / Linda ...Authors: María Pagnon de la Vega / Vilmantas Giedraitis / Wojciech Michno / Lena Kilander / Gökhan Güner / Mara Zielinski / Malin Löwenmark / RoseMarie Brundin / Torsten Danfors / Linda Söderberg / Irina Alafuzoff / Lars N G Nilsson / Anna Erlandsson / Dieter Willbold / Stephan A Müller / Gunnar F Schröder / Jörg Hanrieder / Stefan F Lichtenthaler / Lars Lannfelt / Dag Sehlin / Martin Ingelsson /
Abstract: Point mutations in the amyloid precursor protein gene () cause familial Alzheimer's disease (AD) by increasing generation or altering conformation of amyloid β (Aβ). Here, we describe the mutation ...Point mutations in the amyloid precursor protein gene () cause familial Alzheimer's disease (AD) by increasing generation or altering conformation of amyloid β (Aβ). Here, we describe the mutation (Δ690-695), the first reported deletion causing autosomal dominant AD. Affected individuals have an age at symptom onset in their early forties and suffer from a rapidly progressing disease course. Symptoms and biomarkers are typical of AD, with the exception of normal cerebrospinal fluid (CSF) Aβ42 and only slightly pathological amyloid-positron emission tomography signals. Mass spectrometry and Western blot analyses of patient CSF and media from experimental cell cultures indicate that the mutation alters APP processing by increasing β-secretase cleavage and affecting α-secretase cleavage. Furthermore, in vitro aggregation studies and analyses of patient brain tissue samples indicate that the longer form of mutated Aβ, AβUpp1-42, accelerates the formation of fibrils with unique polymorphs and their deposition into amyloid plaques in the affected brain.
History
DepositionMar 10, 2021-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
UpdateOct 13, 2021-
Current statusOct 13, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0178
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0178
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12592.png

Downloads & links

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Map

FileDownload / File: emd_12592.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAbeta36 - polymorph 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 200 pix.
= 167.8 Å		0.84 Å/pix.
x 200 pix.
= 167.8 Å		0.84 Å/pix.
x 200 pix.
= 167.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0178 / Movie #1: 0.0178
Minimum - Maximum-0.004990329 - 0.033714596
Average (Standard dev.)0.0022425286 (±0.0058043487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 167.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8390.8390.839
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z167.800167.800167.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0050.0340.002

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Supplemental data

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Sample components

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Entire : amyloid fibril of Abeta36

EntireName: amyloid fibril of Abeta36
Components
  • Complex: amyloid fibril of Abeta36
    • Protein or peptide: amyloid-beta

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Supramolecule #1: amyloid fibril of Abeta36

SupramoleculeName: amyloid fibril of Abeta36 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: amyloid-beta

MacromoleculeName: amyloid-beta / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
DAEFRHDSGY EVHHQKLVGS NKGAIIGLMV GGVVIA

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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: 2
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: 20.0 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

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.41 Å
Applied symmetry - Helical parameters - Δ&Phi: 178.45 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66651
Startup modelType of model: OTHER / Details: noise-filled cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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