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    Yorodumi
    - EMDB-5233: CryoEM structure of cytoplasmic polyhedrosis virus -

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    Basic information

    Entry
    Database: EMDB / ID: 5233
    TitleCryoEM structure of cytoplasmic polyhedrosis virus
    Keywordscryoelectron microscopy
    SampleCytoplasmic Polyhedrosis Virus
    SourceCypovirus / virus / CPV
    Map dataThis is a hemi-spherical density map of threefold view of cytoplasmic polyhedrosis virus
    Methodsingle particle (icosahedral) reconstruction, at 3.9 A resolution
    AuthorsCheng L / Sun J / Zhang K / Mou Z / Huang X / Ji G / Sun F / Zhang J / Zhu P
    CitationProc. Natl. Acad. Sci. U.S.A., 2011, 108, 1373-1378

    Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 1373-1378 StrPapers
    Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping.
    Lingpeng Cheng / Jingchen Sun / Kai Zhang / Zongjun Mou / Xiaoxing Huang / Gang Ji / Fei Sun / Jingqiang Zhang / Ping Zhu

    DateDeposition: Sep 14, 2010 / Header (metadata) release: Mar 10, 2011 / Map release: Mar 10, 2011 / Last update: Sep 14, 2010

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 3
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 3
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5233.map.gz (map file in CCP4 format, 800001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    500 pix
    1.19 A/pix
    = 595. A
    640 pix
    1.19 A/pix
    = 761.6 A
    640 pix
    1.19 A/pix
    = 761.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.19 A
    Density
    Contour Level:3 (by author), 3 (movie #1):
    Minimum - Maximum-16.95112991 - 18.03697586
    Average (Standard dev.)0E-8 (1)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions640640500
    Origin-320-3200
    Limit319319499
    Spacing640640500
    CellA: 761.60004 A / B: 761.60004 A / C: 595 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.191.191.19
    M x/y/z640640500
    origin x/y/z0.0000.0000.000
    length x/y/z761.600761.600595.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-99-99-99
    NX/NY/NZ200200200
    MAP C/R/S123
    start NC/NR/NS-320-3200
    NC/NR/NS640640500
    D min/max/mean-16.95118.0370.000

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    Supplemental data

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    Sample components

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    Entire Cytoplasmic Polyhedrosis Virus

    EntireName: Cytoplasmic Polyhedrosis Virus / Number of components: 5

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    Component #1: virus, Cypovirus

    VirusName: Cypovirus / a.k.a: CPV / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
    SpeciesSpecies: Cypovirus / virus / CPV
    Source (natural)Host Species: Bombyx mori / arthropod / / Host category: INVERTEBRATES

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionpH: 7.5
    Support film200 mesh
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Method: Blot for 4 seconds before plunging

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    Electron microscopy imaging

    ImagingMicroscope: FEI TITAN KRIOS / Date: Apr 10, 2010
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: OTHER
    LensMagnification: 75000 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 2800 nm
    Specimen HolderModel: OTHER
    CameraDetector: GENERIC GATAN (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 1600 / Sampling size: 1.19 microns / Bit depth: 24

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 29000 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: cross-common lines / Software: IMIRS / CTF correction: Each micrograph / Resolution: 3.9 A / Resolution method: FSC 0.143

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    Atomic model buiding

    Output model

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