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    Yorodumi
    - EMDB-5122: RNA-releasing poliovirus intermediates -

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    Basic information

    Entry
    Database: EMDB / ID: 5122
    TitleRNA-releasing poliovirus intermediates
    KeywordsPicornavirus / poliovirus / intermediate / RNA-release / 80S
    Sample80S poliovirus
    Sourcepoliovirus 1 mahoney / virus
    Map dataLATE early RNA-releasing 80S poliovirus
    Methodsingle particle (icosahedral) reconstruction, at 10 A resolution
    AuthorsLevy HC / Bostina M / Filman DJ / Hogle JM
    CitationJ. Virol., 2010, 84, 4426-4441

    J. Virol., 2010, 84, 4426-4441 StrPapers
    Catching a virus in the act of RNA release: a novel poliovirus uncoating intermediate characterized by cryo-electron microscopy.
    Hazel C Levy / Mihnea Bostina / David J Filman / James M Hogle

    DateDeposition: Jun 15, 2009 / Header (metadata) release: Jul 31, 2009 / Map release: Mar 10, 2010 / Last update: Jun 15, 2009

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 20.501312207
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 20.501312207
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-3iyc
    • Surface level: 20.501312207
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5122.map.gz (map file in CCP4 format, 31723 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    201 pix
    2.32 A/pix
    = 466.782 A
    201 pix
    2.32 A/pix
    = 466.782 A
    201 pix
    2.32 A/pix
    = 466.782 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.3223 A
    Density
    Contour Level:2 (by author), 20.5013122 (movie #1):
    Minimum - Maximum-29.2078 - 68.0468
    Average (Standard dev.)1.89523 (8.2149)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions201201201
    Origin-100-100-100
    Limit100100100
    Spacing201201201
    CellA=B=C: 466.782 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.32229850746272.32229850746272.3222985074627
    M x/y/z201201201
    origin x/y/z0.0000.0000.000
    length x/y/z466.782466.782466.782
    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/NS201201201
    D min/max/mean-29.20868.0471.895

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    Supplemental data

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    Sample components

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    Entire 80S poliovirus

    EntireName: 80S poliovirus / Details: native virus heat-treated at 56 degrees C / Number of components: 1 / Oligomeric State: 60 promoters arranged as a icosahedron
    MassTheoretical: 8.3 MDa / Experimental: 8.3 MDa / Measured by: Sedimentation

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    Component #1: virus, poliovirus 1 mahoney

    VirusName: poliovirus 1 mahoney / a.k.a: poliovirus 1 mahoney / Class: VIRION / Details: native virus is converted by heat-treatment to 80S / Empty: Yes / Enveloped: No / Isolate: SEROTYPE
    MassTheoretical: 8.3 MDa / Experimental: 8.3 MDa
    SpeciesSpecies: poliovirus 1 mahoney / virus
    Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES
    Shell #1Name of element: capsid / Diameter: 290 A / T number(triangulation number): 1

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.2 mg/ml / Buffer solution: 20mM Tris, 50mM NaCl, 2 mM CaCl2 / pH: 7.4
    Support film200 mesh copper grids
    Stainingnot stained
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: blot for 3 secs / Details: Vitrification instrument: home made plunger

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F30
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: OTHER
    LensMagnification: 59000 X (nominal) / Imaging mode: OTHER / Defocus: 900 - 3000 nm
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 138 / Scanner: ZEISS SCAI / Sampling size: 7 microns

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction
    Details: 10,000 particle were partitioned into two distinct classes
    Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: PFT / Software: PFT2, EM3DR2 / CTF correction: each micrograph / Resolution: 10 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: INSOUT / Refinement protocol: rigid body / Refinement space: RECIPROCAL / Details: Protocol: Rigid Body
    Input PDB model: 1pov
    Output model

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