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- EMDB-5132: The reconstructed F120 amyloid fibril represents the structure of... -

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Basic information

Entry
Database: EMDB / ID: EMD-5132
TitleThe reconstructed F120 amyloid fibril represents the structure of a selected subpopulation from the Abeta(1-40) fibril sample with a mean crossover distance of 120 nm. The F140 subpopulation with a mean crossover distance of 140 nm had been studied and deposited previously (EMDB accession no. 5008).
Map dataCross-sectional density slice of the F120 amyloid fibril of 24 Angstrom thickness. F120 corresponds to a subpopulation of the Abeta(1-40) amyloid fibril sample with a mean crossover distance of 120 nm.
Sample
  • Sample: Human Abeta (1-40)
  • Protein or peptide: AbetaAmyloid beta
KeywordsAlzheimer's disease / micromechanical properties / electron cryo-microscopy / amyloid fibrils
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / negative staining / Resolution: 10.1 Å
AuthorsSachse C / Faendrich M / Grigorieff N
CitationJournal: Angew Chem Int Ed Engl / Year: 2010
Title: Nanoscale flexibility parameters of Alzheimer amyloid fibrils determined by electron cryo-microscopy.
Authors: Carsten Sachse / Nikolaus Grigorieff / Marcus Fändrich /
History
DepositionOct 10, 2009-
Header (metadata) releaseOct 12, 2009-
Map releaseOct 12, 2009-
UpdateMar 2, 2016-
Current statusMar 2, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5132_1.tif

Downloads & links

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Map

FileDownload / File: emd_5132.map.gz / Format: CCP4 / Size: 306.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCross-sectional density slice of the F120 amyloid fibril of 24 Angstrom thickness. F120 corresponds to a subpopulation of the Abeta(1-40) amyloid fibril sample with a mean crossover distance of 120 nm.
Voxel sizeX=Y=Z: 2.4 Å
Density
Contour LevelBy AUTHOR: 1.4 / Movie #1: 1.4
Minimum - Maximum-1.45155275 - 3.52434707
Average (Standard dev.)0.00000001 (±0.9999938)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions4010020
Spacing1004020
CellA: 96.0 Å / B: 240.00002 Å / C: 48.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.42.42.4
M x/y/z4010020
origin x/y/z0.0000.0000.000
length x/y/z96.000240.00048.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS1004020
D min/max/mean-1.4523.5240.000

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Supplemental data

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Sample components

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Entire : Human Abeta (1-40)

EntireName: Human Abeta (1-40)
Components
  • Sample: Human Abeta (1-40)
  • Protein or peptide: AbetaAmyloid beta

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Supramolecule #1000: Human Abeta (1-40)

SupramoleculeName: Human Abeta (1-40) / type: sample / ID: 1000 / Oligomeric state: helical / Number unique components: 1
Molecular weightTheoretical: 4.33 KDa

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Macromolecule #1: Abeta

MacromoleculeName: Abeta / type: protein_or_peptide / ID: 1 / Name.synonym: Abeta / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 8.7 / Details: 50 mM Borate
StainingType: NEGATIVE / Details: Blot for 7 seconds before plunging
GridDetails: Quantifoil 400 mesh 1.3 micrometer holes
VitrificationCryogen name: ETHANE / Chamber temperature: 77.2 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: custom-built plunging apparatus. in coldroom at 277 K.
Method: Blot for 7 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 58333 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.9 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 93 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 200,000 times magnification
DateNov 9, 2005
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 62 / Average electron dose: 35 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle CTFTILT
Final angle assignmentDetails: one-degree sampling around helical axis, out-of-plane tilt 16 degree deviation (in 1 degree steps)
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.8 Å
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.1 Å / Resolution method: OTHER / Software - Name: SPIDER
DetailsThe fibrils in the sample were selected based on their uniform width. 2. The F120 subset of limited crossover distances (110-130 nm) was chosen for the reconstruction.

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