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    - EMDB-5133: 17 angstrom of wild Rabbit Hemorrhagic DiseaseVirus core-like par... -

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    Basic information

    Entry
    Database: EMDB / ID: 5133
    Title17 angstrom of wild Rabbit Hemorrhagic DiseaseVirus core-like particle cryomicroscopy structure
    KeywordsRHDV / vp60 / vp10 / core-like particles
    Samplewild Rabbit Hemorrhagic Disease Viruses core-like particles
    Sourcerabbit hemorrhagic disease virus core like particles / virus
    Map dataThis is the cryo-electron microscopy reconstruction of the wild rabbit hemorrhagic disease virus core-like particles.
    Methodsingle particle (icosahedral) reconstruction, at 17 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 11, 2009 / Header (metadata) release: Oct 15, 2009 / Map release: Aug 12, 2010 / Last update: Oct 11, 2009

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_5133.map.gz (map file in CCP4 format, 16001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    160 pix
    2.54 A/pix
    = 406.4 A
    160 pix
    2.54 A/pix
    = 406.4 A
    160 pix
    2.54 A/pix
    = 406.4 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:1.7 (by author), 1 (movie #1):
    Minimum - Maximum-1.95755 - 3.63758
    Average (Standard dev.)0.0550003 (0.848303)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions160160160
    Origin-80-80-80
    Limit797979
    Spacing160160160
    CellA=B=C: 406.4 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.542.542.54
    M x/y/z160160160
    origin x/y/z0.0000.0000.000
    length x/y/z406.400406.400406.400
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-34-26-72
    NX/NY/NZ6953145
    MAP C/R/S123
    start NC/NR/NS-80-80-80
    NC/NR/NS160160160
    D min/max/mean-1.9583.6380.055

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    Supplemental data

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    Sample components

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    Entire wild Rabbit Hemorrhagic Disease Viruses core-like particles

    EntireName: wild Rabbit Hemorrhagic Disease Viruses core-like particles
    Number of components: 3 / Oligomeric State: icosahedral
    MassTheoretical: 7.2 MDa

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    Component #1: virus, rabbit hemorrhagic disease virus core like particles

    VirusName: rabbit hemorrhagic disease virus core like particles / a.k.a: rabbit hemorrhagic disease virus core like particles / Class: VIROID / Empty: No / Enveloped: No / Isolate: SPECIES
    MassTheoretical: 7.2 MDa
    SpeciesSpecies: rabbit hemorrhagic disease virus core like particles / virus
    Source (natural)Host Species: Oryctolagus cuniculus / mammal / / Host category: VERTEBRATES
    Shell #1Name of element: S / Diameter: 320 A / T number(triangulation number): 3

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Support film300 mesh holygrid
    VitrificationInstrument: NONE / Cryogen name: ETHANE
    Method: Embeded in thin layer of vitreous ice on freshly carbon-coated home-made holey EM grid by 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: GATAN HELIUM / Temperature: 105 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 230 / Sampling size: 12.7 microns / Bit depth: 16

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of class averages: 21 / Number of projections: 895 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: shadow matching method / Software: Eman spider / CTF correction: Each particle / Resolution: 17 A / Resolution method: FSC 0.5

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    Atomic model buiding

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

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