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    Yorodumi
    - EMDB-1307: Electron cryotomography reveals the portal in the herpesvirus capsid. -

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    Basic information

    Entry
    Database: EMDB / ID: 1307
    TitleElectron cryotomography reveals the portal in the herpesvirus capsid.
    SampleHerpes Simplex Virus 1
    SourceHuman herpesvirus 1 / virus / Herpes Simplex
    Map dataThis is the 5-fold-averaged map.
    Methodsubtomogram averaging
    AuthorsChang JT / Schmid MF / Rixon FJ / Chiu W
    CitationJ. Virol., 2007, 81, 2065-2068

    J. Virol., 2007, 81, 2065-2068 StrPapers
    Electron cryotomography reveals the portal in the herpesvirus capsid.
    Juan T Chang / Michael F Schmid / Frazer J Rixon / Wah Chiu

    DateDeposition: Nov 25, 2006 / Header (metadata) release: Dec 6, 2006 / Map release: Dec 6, 2007 / Last update: Nov 25, 2006

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.12
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 0.12
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1307.map.gz (map file in CCP4 format, 93313 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    288 pix
    5.43 A/pix
    = 1563.84 A
    288 pix
    5.43 A/pix
    = 1563.84 A
    288 pix
    5.43 A/pix
    = 1563.84 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 5.43 A
    Density
    Contour Level:0.119, 0.12 (movie #1):
    Minimum - Maximum-0.232214 - 0.370385
    Average (Standard dev.)-0.0147267 (0.0501588)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions288288288
    Origin-144-144-144
    Limit143143143
    Spacing288288288
    CellA=B=C: 1563.84 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z5.435.435.43
    M x/y/z288288288
    origin x/y/z0.0000.0000.000
    length x/y/z1563.8401563.8401563.840
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-184-184-183
    NX/NY/NZ368368368
    MAP C/R/S123
    start NC/NR/NS-144-144-144
    NC/NR/NS288288288
    D min/max/mean-0.2320.370-0.015

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    Supplemental data

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    Sample components

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    Entire Herpes Simplex Virus 1

    EntireName: Herpes Simplex Virus 1 / Number of components: 1

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    Component #1: virus, Human herpesvirus 1

    VirusName: Human herpesvirus 1 / a.k.a: Herpes Simplex / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: SPECIES
    SpeciesSpecies: Human herpesvirus 1 / virus / Herpes Simplex
    Source (natural)Host Species: Homo sapiens / human / Host category: INVERTEBRATES
    Shell #1Name of element: Capsid / Diameter: 1250 A / T number(triangulation number): 16

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    Experimental details

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    Sample preparation

    Sample solutionBuffer solution: 170mM NaCl, 3.4mM KCl, 10mM Na2HPO4, 1.8mM KH2PO4, 6.8mM CaCl2, 4.9mM MgCl2
    pH: 7.2
    Support film200 mesh copper grid
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 % / Details: Vitrification instrument: Vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 2010F
    Details: Tilted from -70 to +70 in 2 degree increments using Mr T software (unpublished).
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 50 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 20000 X (nominal), 27680 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 3000 nm
    Specimen HolderHolder: Side entry liquid nitrogen cooled / Model: GATAN LIQUID NITROGEN / Tilt Angle: 70 - 70 deg. / Temperature: 93 K ( 93 - 93 K)
    CameraDetector: GENERIC GATAN

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    Image processing

    ProcessingMethod: subtomogram averaging
    Details: Averaged 13 particles extracted from the reconstruction. Average number of tilts used in the 3D reconstructions: 71. Average tomographic tilt angle increment: 2.
    3D reconstructionAlgorithm: Weighted backprojection / Software: IMOD / Details: 5-fold-averaged

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