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    Yorodumi
    - EMDB-1650: Reconstruction of a 13 nm wide Abeta(1-40) amyloid fibril -

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    Basic information

    Entry
    Database: EMDB / ID: 1650
    TitleReconstruction of a 13 nm wide Abeta(1-40) amyloid fibril
    KeywordsAlzheimer's disease / amyloid / prion / protein folding
    SampleAbeta(1-40) amyloid fibril
    SourceHomo sapiens / human
    Map dataThis is a reconstruction of an Abeta(1-40) amyloid fibril
    Methodhelical reconstruction, at 23 A resolution
    AuthorsSchmidt M / Sachse C / Richter W / Xu C / Fandrich M / Grigorieff N
    CitationProc. Natl. Acad. Sci. U.S.A., 2009, 106, 19813-19818

    Proc. Natl. Acad. Sci. U.S.A., 2009, 106, 19813-19818 StrPapers
    Comparison of Alzheimer Abeta(1-40) and Abeta(1-42) amyloid fibrils reveals similar protofilament structures.
    Matthias Schmidt / Carsten Sachse / Walter Richter / Chen Xu / Marcus Fändrich / Nikolaus Grigorieff

    DateDeposition: Sep 11, 2009 / Header (metadata) release: Sep 24, 2009 / Map release: Sep 24, 2009 / Last update: Sep 11, 2009

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.1
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 0.1
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1650.map.gz (map file in CCP4 format, 64 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    10 pix
    4.8 A/pix
    = 48. A
    40 pix
    4.8 A/pix
    = 192. A
    40 pix
    4.8 A/pix
    = 192. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 4.8 A
    Density
    Contour Level:0.055 (by author), 0.1 (movie #1):
    Minimum - Maximum-0.313765 - 0.515397
    Average (Standard dev.)0.00522568 (0.124983)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions404010
    Origin000
    Limit39399
    Spacing404010
    CellA: 192 A / B: 192 A / C: 48 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/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
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ
    NX/NY/NZ
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS404010
    D min/max/mean-0.3140.5150.005

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    Supplemental data

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    Sample components

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    Entire Abeta(1-40) amyloid fibril

    EntireName: Abeta(1-40) amyloid fibril / Number of components: 1 / Oligomeric State: Cross-beta structure

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    Component #1: protein, Abeta(1-40) peptide

    ProteinName: Abeta(1-40) peptide / a.k.a: Alzheimer peptide / Oligomeric Details: Cross-beta / Recombinant expression: Yes
    MassTheoretical: 4.33 kDa
    SourceSpecies: Homo sapiens / human

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    Experimental details

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    Sample preparation

    Specimen statehelical array
    Helical parametersAxial symmetry: C2 (2 fold cyclic) / Hand: LEFT HANDED
    Crystal grow detailsIncubation for 4 days at 4 degC
    Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: 50 mM sodium borate / pH: 8.7
    Support film400 mesh copper grid
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 30 % / Method: One-sided blotting for 5 seconds before plunging
    Details: Vitrification instrument: Manual plunger (Brandeis)

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F30
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 59000 X (nominal), 58090 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 3500 nm
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 90 K ( 90 - 90 K)
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 4 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 12 / OD range: 1.2

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    Image processing

    ProcessingMethod: helical reconstruction / Details: Fibrils were selected using BOXER
    3D reconstructionAlgorithm: Weighted back projection / Software: Spider / CTF correction: Each particle / Details: Final map was calculated from 4 fibrils / Resolution: 23 A / Resolution method: FSC 0.5

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