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    Yorodumi
    - EMDB-5184: The structure of JC polyomavirus treated with 250 mM L-arginine (... -

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    Basic information

    Entry
    Database: EMDB / ID: 5184
    TitleThe structure of JC polyomavirus treated with 250 mM L-arginine (pH 10.7)
    KeywordsJC / JCV / polyomavirus / arginine
    SampleJC polyomavirus in buffer A with 250 mM L-arginine (pH 10.7)
    SourceJC polyomavirus / virus / JCV
    Map dataCryo-EM based reconstruction of JC polyomavirus treated with 250 mM L-arginine
    Methodsingle particle (icosahedral) reconstruction, at 17.6 A resolution
    AuthorsShen PS / Enderlein D / Nelson C / Carter WS / Kawano M / Xing L / Swenson RD / Olson NH / Baker TS / Cheng RH / Atwood WJ / Johne R / Belnap DM
    CitationVirology, 2011, 411, 142-152

    Virology, 2011, 411, 142-152 StrPapers
    The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4.
    Peter S Shen / Dirk Enderlein / Christian D S Nelson / Weston S Carter / Masaaki Kawano / Li Xing / Robert D Swenson / Norman H Olson / Timothy S Baker / R Holland Cheng / Walter J Atwood / Reimar Johne / David M Belnap

    DateDeposition: Apr 12, 2010 / Header (metadata) release: Dec 8, 2010 / Map release: Jan 19, 2011 / Last update: Apr 12, 2010

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 26
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 26
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_5184.map.gz (map file in CCP4 format, 193091 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    367 pix
    1.59 A/pix
    = 597.84 A
    367 pix
    1.59 A/pix
    = 597.84 A
    367 pix
    1.59 A/pix
    = 597.84 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.59 A
    Density
    Contour Level:26 (by author), 26 (movie #1):
    Minimum - Maximum-23.6142 - 78.3666
    Average (Standard dev.)8.0241 (18.0072)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions367367367
    Origin-183-183-183
    Limit183183183
    Spacing367367367
    CellA=B=C: 597.84 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.591.591.59
    M x/y/z376376376
    origin x/y/z0.0000.0000.000
    length x/y/z597.840597.840597.840
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-34-26-72
    NX/NY/NZ6953145
    MAP C/R/S123
    start NC/NR/NS-183-183-183
    NC/NR/NS367367367
    D min/max/mean-23.61478.3678.024

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    Supplemental data

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    Sample components

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    Entire JC polyomavirus in buffer A with 250 mM L-arginine (pH 10.7)

    EntireName: JC polyomavirus in buffer A with 250 mM L-arginine (pH 10.7)
    Number of components: 1 / Oligomeric State: virions

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    Component #1: virus, JC polyomavirus

    VirusName: JC polyomavirus / a.k.a: JCV / Class: VIRION / Details: Cryo-EM of JC polyomavirus over holey carbon grids / Empty: No / Enveloped: No / Isolate: STRAIN
    SpeciesSpecies: JC polyomavirus / virus / JCV
    Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES
    Shell #1Name of element: VP1 / Diameter: 5000 A / T number(triangulation number): 7

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 1.5 mg/ml
    Buffer solution: 10 mM Tris, 50 mM NaCl, 0.01 mM CaCl2, 250 mM L-arginine
    pH: 10.7
    Support film200 mesh copper grid (holey carbon)
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 89 K / Humidity: 100 % / Method: 3 second blot before plunging
    Details: Vitrification instrument: Vitrobot. vitrification carried out in nitrogen atmosphere

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F30 / Date: Apr 23, 2007
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
    LensMagnification: 39000 X (nominal), 39000 X (calibrated)
    Astigmatism: astigmatism was corrected at 59,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 4900 nm
    Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
    Model: GATAN LIQUID NITROGEN / Temperature: 90 K ( 88 - 95 K)
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 50 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 16 / Details: Micrographs digitized in positive contrast mode.

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: common lines / Software: PFT2 and EM3DR2 / CTF correction: each micrograph / Resolution: 17.6 A / Resolution method: FSC 0.333

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