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    Yorodumi
    - EMDB-1421: Electron cryomicroscopy reveals different F1+F2 protein States in... -

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    Basic information

    Entry
    Database: EMDB / ID: 1421
    TitleElectron cryomicroscopy reveals different F1+F2 protein States in intact parainfluenza virions.
    SampleF-Protein in intact Parainfluenzavirus 5
    SourceParainfluenza virus 5 / virus
    Map dataIn-situ 3D reconstruction of the ectodomain of the PIV5 F protein determined from cryo-negative stain electron micrographs
    Methodsingle particle reconstruction, at 15 A resolution
    AuthorsLudwig K / Schade B / Boettcher C / Korte T
    CitationJ. Virol., 2008, 82, 3775-3781

    J. Virol., 2008, 82, 3775-3781 StrPapers
    Electron cryomicroscopy reveals different F1+F2 protein States in intact parainfluenza virions.
    Kai Ludwig / Boris Schade / Christoph Böttcher / Thomas Korte / Nina Ohlwein / Bolormaa Baljinnyam / Michael Veit / Andreas Herrmann

    DateDeposition: Sep 7, 2007 / Header (metadata) release: Sep 11, 2007 / Map release: Apr 7, 2008 / Last update: Sep 7, 2007

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: -100
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: -100
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1421.map.gz (map file in CCP4 format, 1301 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    110 pix
    1.56 A/pix
    = 171.6 A
    110 pix
    1.56 A/pix
    = 171.6 A
    110 pix
    1.56 A/pix
    = 171.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.56 A
    Density
    Contour Level:-95 (by emdb), -100 (movie #1):
    Minimum - Maximum-128 - 122
    Average (Standard dev.)-124.687 (18.0757)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions110110110
    Origin-55-54-55
    Limit545554
    Spacing110110110
    CellA=B=C: 171.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
    A/pix X/Y/Z1.561.561.56
    M x/y/z110110110
    origin x/y/z0.0000.0000.000
    length x/y/z171.600171.600171.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-30-30-49
    NX/NY/NZ6060100
    MAP C/R/S123
    start NC/NR/NS-54-55-55
    NC/NR/NS110110110
    D min/max/mean-128.000122.000-124.687

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    Supplemental data

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    Sample components

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    Entire F-Protein in intact Parainfluenzavirus 5

    EntireName: F-Protein in intact Parainfluenzavirus 5
    Details: sample of fusion active virions (proven by fluorescence spectroscopy)of PIV5 (strain W3A)
    Number of components: 1 / Oligomeric State: F-Protein Homotrimer
    MassTheoretical: 150 kDa

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    Component #1: protein, F-Protein

    ProteinName: F-Protein / Oligomeric Details: Homotrimer / Recombinant expression: No
    MassExperimental: 150 kDa
    SourceSpecies: Parainfluenza virus 5 / virus / Strain: W3A
    Source (natural)Location in cell: viral membrane

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: PBS (150 mM NaCl, 5.8 mM NaH2PO4/Na2HPO4) / pH: 7.4
    Support film200 mesh carbon coated collodium-supported copper grids
    Staining30 seconds absorption 60 seconds staining (1% phospho-tungstic acid, pH 7.4) vitrified in liquid ethane
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
    Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a redetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen,and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.
    Details: Vitrification instrument: self-construction

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Electron dose: 12 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 51064 X (calibrated)
    Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1501 - 2066 nm
    Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
    Model: GATAN LIQUID NITROGEN / Temperature: 92 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 175 / Scanner: PRIMESCAN / Sampling size: 4 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 5700
    Details: well resolved spike-like proteins protruding from the viral membrane suitable for single particle analysis were interactively selected
    Applied symmetry: C3 (3 fold cyclic)
    3D reconstructionAlgorithm: Common lines / Software: Imagic / CTF correction: MSA-based / Resolution: 15 A / Resolution method: FSC 3 SIGMA

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