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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: 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).
    KeywordsAlzheimer's disease / micromechanical properties / electron cryo-microscopy / amyloid fibrils
    SampleHuman Abeta (1-40)
    SourceHomo sapiens / human
    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.
    Methodhelical reconstruction, at 10.1 A resolution
    AuthorsSachse C / Faendrich M / Grigorieff N
    CitationAngew. Chem. Int. Ed. Engl., 2010, 49, 1321-1323

    Angew. Chem. Int. Ed. Engl., 2010, 49, 1321-1323 StrPapers
    Nanoscale flexibility parameters of Alzheimer amyloid fibrils determined by electron cryo-microscopy.
    Carsten Sachse / Nikolaus Grigorieff / Marcus Fändrich

    DateDeposition: Oct 10, 2009 / Header (metadata) release: Oct 12, 2009 / Map release: Oct 12, 2009 / Last update: Oct 10, 2009

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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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    Supplemental images

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    Map

    Fileemd_5132.map.gz (map file in CCP4 format, 314 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    20 pix
    2.4 A/pix
    = 48. A
    40 pix
    2.4 A/pix
    = 240. A
    100 pix
    2.4 A/pix
    = 96. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.4 A
    Density
    Contour Level:1.4 (by author), 1.4 (movie #1):
    Minimum - Maximum-1.45155275 - 3.52434707
    Average (Standard dev.)1E-8 (0.9999938)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions4010020
    Origin000
    Limit399919
    Spacing1004020
    CellA: 96 A / B: 240.00002 A / C: 48 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/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
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ
    NX/NY/NZ
    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) / Number of components: 1 / Oligomeric State: helical
    MassTheoretical: 4.33 kDa

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    Component #1: protein, Abeta

    ProteinName: Abeta / a.k.a: Abeta / Recombinant expression: No
    SourceSpecies: Homo sapiens / human

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    Experimental details

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    Sample preparation

    Specimen statefilament
    Helical parametersAxial symmetry: C2 (2 fold cyclic) / Hand: LEFT HANDED / Delta z: 4.8 A
    Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: 50 mM Borate / pH: 8.7
    Support filmQuantifoil 400 mesh 1.3 micrometer holes
    StainingBlot for 7 seconds before plunging
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 77.2 K / Method: Blot for 7 seconds before plunging
    Details: Vitrification instrument: custom-built plunging apparatus. in coldroom at 277 K.

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F30 / Date: Nov 9, 2005
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 59000 X (nominal), 58333 X (calibrated)
    Astigmatism: objective lens astigmatism was corrected at 200,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1900 - 3500 nm
    Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
    Model: GATAN LIQUID NITROGEN / Temperature: 93 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 62 / Scanner: ZEISS SCAI / Sampling size: 7 microns

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    Image processing

    ProcessingMethod: helical reconstruction
    Details: The 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.
    3D reconstructionAlgorithm: iterative algebraic reconstruction
    Euler angles: one-degree sampling around helical axis, out-of-plane tilt 16 degree deviation (in 1 degree steps)
    Software: SPIDER / CTF correction: Each particle CTFTILT / Resolution: 10.1 A / Resolution method: 10.1

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