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    Yorodumi
    - EMDB-1437: Sindbis virus conformational changes induced by a neutralizing an... -

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    Basic information

    Entry
    Database: EMDB / ID: 1437
    TitleSindbis virus conformational changes induced by a neutralizing anti-E1 monoclonal antibody.
    SampleSin-33 Fab treated Sindbis virus
    SourceUnidentified
    Sindbis virus / virus
    Map dataangel
    Methodsingle particle (icosahedral) reconstruction, at 24 A resolution
    AuthorsParedes AM / Hernandez R / West M / Brown DT
    CitationJ. Virol., 2008, 82, 5750-5760

    J. Virol., 2008, 82, 5750-5760 StrPapers
    Sindbis virus conformational changes induced by a neutralizing anti-E1 monoclonal antibody.
    Raquel Hernandez / Angel Paredes / Dennis T Brown

    DateDeposition: Sep 24, 2007 / Header (metadata) release: Oct 2, 2007 / Map release: Apr 23, 2008 / Last update: Sep 24, 2007

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1.2
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 1.2
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1437.map.gz (map file in CCP4 format, 65537 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    256 pix
    2.5 A/pix
    = 640. A
    256 pix
    2.5 A/pix
    = 640. A
    256 pix
    2.5 A/pix
    = 640. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.5 A
    Density
    Contour Level:2.31, 1.2 (movie #1):
    Minimum - Maximum-6.94307 - 5.38466
    Average (Standard dev.)5.7768e-10 (1)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions256256256
    Origin-128-128-128
    Limit127127127
    Spacing256256256
    CellA=B=C: 640 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.52.52.5
    M x/y/z256256256
    origin x/y/z0.0000.0000.000
    length x/y/z640.000640.000640.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-60-60-59
    NX/NY/NZ120120120
    MAP C/R/S123
    start NC/NR/NS-128-128-128
    NC/NR/NS256256256
    D min/max/mean-6.9435.3850.000

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    Supplemental data

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    Sample components

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    Entire Sin-33 Fab treated Sindbis virus

    EntireName: Sin-33 Fab treated Sindbis virus / Number of components: 2
    MassTheoretical: 45 MDa / Measured by: STEM mass measurements Brookhaven, NY.

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    Component #1: protein, Fab

    ProteinName: Fab / Oligomeric Details: monomer / Recombinant expression: Yes
    SourceSpecies: Unidentified

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    Component #2: virus, Sindbis virus

    VirusName: Sindbis virus / Class: VIRION / Isolate: STRAIN / Empty: No / Enveloped: Yes
    SpeciesSpecies: Sindbis virus / virus
    Source (natural)Host Species: Culex / arthropod / Host category: INVERTEBRATES
    Shell #1Name of element: Envelope / Diameter: 680 A / T number(triangulation number): 4
    Shell #2Name of element: Nucleocapsid / Diameter: 400 A / T number(triangulation number): 4

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 20 mM MOPS, 100 mM NaCl / pH: 7.4
    Support filmholey carbon film
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 110 K / Method: Blot holey carbon grid from behind / Details: Vitrification instrument: plunger

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 4000EX
    Electron gunElectron source: LAB6 / Accelerating voltage: 400 kV / Electron dose: 5 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal)
    Astigmatism: objective lens astigmatism was corrected at 60,000 times magnification
    Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3000 nm
    Specimen HolderHolder: Side entry liquid nitrogen cooled / Model: GATAN LIQUID NITROGEN / Temperature: 110 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 6 / Scanner: ZEISS SCAI / Sampling size: 16 microns

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 858 / Number of class averages: 19 / Applied symmetry: I (icosahedral)
    3D reconstructionSoftware: MRC / CTF correction: CTF correction of each particle / Resolution: 24 A / Resolution method: FSC
    Details: Final map was calculated from 19 class averages using EMAN and imposing icosahedral symmetry

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