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    Yorodumi
    - EMDB-5131: 10.5 angstrom of Rabbit Hemorrhagic Disease Virus(RHDV)cryomicros... -

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    Basic information

    Entry
    Database: EMDB / ID: 5131
    Title10.5 angstrom of Rabbit Hemorrhagic Disease Virus(RHDV)cryomicroscopy structure
    KeywordsRHDV / vp60 / vp10
    SampleWild Rabbit Hemorrhagic Disease Viruses
    Sourcerabbit hemorrhagic disease viruses / virus
    Map dataThis is the cryo-electron microscopy reconstruction of the wild rabbit hemorrhagic disease virus
    Methodsingle particle (icosahedral) reconstruction, at 10.5 A resolution
    AuthorsHu Z / Tian X / Zhai Y / Xu W / Zheng D / Sun F
    CitationProtein Cell, 2010, 1, 48-58

    Protein Cell, 2010, 1, 48-58 StrPapers
    Cryo-electron microscopy reconstructions of two types of wild rabbit hemorrhagic disease viruses characterized the structural features of Lagovirus.
    Zhongjun Hu / Xiaojuan Tian / Yujia Zhai / Wei Xu / Dong Zheng / Fei Sun

    DateDeposition: Oct 8, 2009 / Header (metadata) release: Oct 15, 2009 / Map release: Aug 12, 2010 / Last update: Oct 8, 2009

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1.15
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 1.15
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_5131.map.gz (map file in CCP4 format, 31251 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    200 pix
    2.54 A/pix
    = 508. A
    200 pix
    2.54 A/pix
    = 508. A
    200 pix
    2.54 A/pix
    = 508. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.54 A
    Density
    Contour Level:1.15 (by author), 1.15 (movie #1):
    Minimum - Maximum-4.19832 - 5.0759
    Average (Standard dev.)-0.012319 (0.714993)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions200200200
    Origin-100-100-100
    Limit999999
    Spacing200200200
    CellA=B=C: 508 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.542.542.54
    M x/y/z200200200
    origin x/y/z0.0000.0000.000
    length x/y/z508.000508.000508.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-34-26-72
    NX/NY/NZ6953145
    MAP C/R/S123
    start NC/NR/NS-100-100-100
    NC/NR/NS200200200
    D min/max/mean-4.1985.076-0.012

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    Supplemental data

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    Sample components

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    Entire Wild Rabbit Hemorrhagic Disease Viruses

    EntireName: Wild Rabbit Hemorrhagic Disease Viruses / Number of components: 3 / Oligomeric State: Icosahedral
    MassTheoretical: 13 MDa

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    Component #1: virus, rabbit hemorrhagic disease viruses

    VirusName: rabbit hemorrhagic disease viruses / a.k.a: rabbit hemorrhagic disease viruses / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
    MassTheoretical: 1.3GDa
    SpeciesSpecies: rabbit hemorrhagic disease viruses / virus
    Source (natural)Host Species: Oryctolagus cuniculus / mammal / / Host category: VERTEBRATES

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Support film300 mesh holygrid
    VitrificationInstrument: NONE / Cryogen name: ETHANE
    Method: Manually blotting the grids with filter paper and then plunging into liquid ethane cooled by liquid nitrogen

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 20
    Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 4000 nm
    Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC / Temperature: 105 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 230 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 12.7 microns / Bit depth: 16

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 15890 / Applied symmetry: I (icosahedral)
    3D reconstructionSoftware: Eman, Spider / CTF correction: Each particle / Resolution: 10.5 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: chimera / Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: Rigid Body
    Input PDB model: 2GH8

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