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- EMDB-1649: Electron cryo-microscopy of an Abeta(1-42) amyloid fibril -

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Basic information

Entry
Database: EMDB / ID: EMD-1649
TitleElectron cryo-microscopy of an Abeta(1-42) amyloid fibril
Map dataThis is a reconstruction of an Abeta(1-42) amyloid fibril
Sample
  • Sample: Abeta(1-42) amyloid fibril
  • Protein or peptide: Abeta(1-42) peptide
KeywordsAlzheimer's disease / amyloid / prion / protein folding
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsSchmidt M / Sachse C / Richter W / Xu C / Fandrich M / Grigorieff N
CitationJournal: Proc Natl Acad Sci U S A / Year: 2009
Title: Comparison of Alzheimer Abeta(1-40) and Abeta(1-42) amyloid fibrils reveals similar protofilament structures.
Authors: Matthias Schmidt / Carsten Sachse / Walter Richter / Chen Xu / Marcus Fändrich / Nikolaus Grigorieff /
Abstract: We performed mass-per-length (MPL) measurements and electron cryomicroscopy (cryo-EM) with 3D reconstruction on an Abeta(1-42) amyloid fibril morphology formed under physiological pH conditions. The ...We performed mass-per-length (MPL) measurements and electron cryomicroscopy (cryo-EM) with 3D reconstruction on an Abeta(1-42) amyloid fibril morphology formed under physiological pH conditions. The data show that the examined Abeta(1-42) fibril morphology has only one protofilament, although two protofilaments were observed with a previously studied Abeta(1-40) fibril. The latter fibril was resolved at 8 A resolution showing pairs of beta-sheets at the cores of the two protofilaments making up a fibril. Detailed comparison of the Abeta(1-42) and Abeta(1-40) fibril structures reveals that they share an axial twofold symmetry and a similar protofilament structure. Furthermore, the MPL data indicate that the protofilaments of the examined Abeta(1-40) and Abeta(1-42) fibrils have the same number of Abeta molecules per cross-beta repeat. Based on this data and the previously studied Abeta(1-40) fibril structure, we describe a model for the arrangement of peptides within the Abeta(1-42) fibril.
History
DepositionSep 11, 2009-
Header (metadata) releaseSep 24, 2009-
Map releaseSep 24, 2009-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.120453838
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.120453838
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1649.tif

Downloads & links

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Map

FileDownload / File: emd_1649.map.gz / Format: CCP4 / Size: 62.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a reconstruction of an Abeta(1-42) amyloid fibril
Voxel sizeX=Y=Z: 4.8 Å
Density
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.1204538
Minimum - Maximum-0.0553911 - 0.214284
Average (Standard dev.)0.00727761 (±0.0427153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions404010
Spacing404010
CellA: 192 Å / B: 192 Å / C: 48 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.84.84.8
M x/y/z404010
origin x/y/z0.0000.0000.000
length x/y/z192.000192.00048.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS404010
D min/max/mean-0.0550.2140.007

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Supplemental data

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Sample components

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Entire : Abeta(1-42) amyloid fibril

EntireName: Abeta(1-42) amyloid fibril
Components
  • Sample: Abeta(1-42) amyloid fibril
  • Protein or peptide: Abeta(1-42) peptide

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Supramolecule #1000: Abeta(1-42) amyloid fibril

SupramoleculeName: Abeta(1-42) amyloid fibril / type: sample / ID: 1000 / Oligomeric state: Cross-beta structure / Number unique components: 1

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Macromolecule #1: Abeta(1-42) peptide

MacromoleculeName: Abeta(1-42) peptide / type: protein_or_peptide / ID: 1 / Name.synonym: Alzheimer peptide / Oligomeric state: Cross-beta / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 4.514 KDa

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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

Concentration1 mg/mL
BufferpH: 7.4 / Details: 50 mM Tris-HCl
GridDetails: 400 mesh copper grids
VitrificationCryogen name: ETHANE / Chamber humidity: 30 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Manual plunger (Brandeis)
Method: One-sided blotting for 5 seconds before plunging
DetailsIncubation for 2 days at room temperature

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 58090 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.75 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 90 K / Max: 90 K / Average: 90 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Number real images: 14 / Average electron dose: 30 e/Å2 / Od range: 1.2 / Bits/pixel: 12
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Details: Final map was calculated from 14 fibril images
DetailsThe fibrils were selected using BOXER

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