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    - EMDB-5280: Poliovirus 135S particle and P1 Fab complex at 12-angs. resolution -

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    Basic information

    Entry
    Database: EMDB / ID: 5280
    TitlePoliovirus 135S particle and P1 Fab complex at 12-angs. resolution
    Keywordspicornavirus / viral cell entry / viral uncoating / virus-antibody complex / virus-Fab complex / virus disassembly / virus uncoating / virus conformational transitions / monospecific antibody
    SamplePoliovirus 135S particle and P1(monospecific antibody) Fab complex
    SourceHuman poliovirus 1 Mahoney / virus / poliovirus 135S
    Map dataThis is a map of poliovirus 135S and P1 Fab complex at 12-ang resolution
    Methodsingle particle (icosahedral) reconstruction, at 12 A resolution
    AuthorsLin J / Cheng N / Chow M / Filman DJ / Steven AC / Hogle JM / Belnap DM
    CitationJ. Virol., 2011, 85, 9974-9983

    J. Virol., 2011, 85, 9974-9983 StrPapers
    An externalized polypeptide partitions between two distinct sites on genome-released poliovirus particles.
    Jun Lin / Naiqian Cheng / Marie Chow / David J Filman / Alasdair C Steven / James M Hogle / David M Belnap

    DateDeposition: May 2, 2011 / Header (metadata) release: May 5, 2011 / Map release: Mar 8, 2012 / Last update: May 2, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 8.6
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 8.6
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5280.map.gz (map file in CCP4 format, 74354 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    267 pix
    1.83 A/pix
    = 488.61 A
    267 pix
    1.83 A/pix
    = 488.61 A
    267 pix
    1.83 A/pix
    = 488.61 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.83 A
    Density
    Contour Level:8.6 (by author), 8.6 (movie #1):
    Minimum - Maximum-31.67783546 - 96.89107513
    Average (Standard dev.)5.0518713 (17.71579361)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions267267267
    Origin-133-133-133
    Limit133133133
    Spacing267267267
    CellA=B=C: 488.61002 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.831.831.83
    M x/y/z267267267
    origin x/y/z0.0000.0000.000
    length x/y/z488.610488.610488.610
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-133-133-133
    NC/NR/NS267267267
    D min/max/mean-31.67896.8915.052

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    Supplemental data

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    Sample components

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    Entire Poliovirus 135S particle and P1(monospecific antibody) Fab complex

    EntireName: Poliovirus 135S particle and P1(monospecific antibody) Fab complex
    Number of components: 2 / Oligomeric State: 135S particle icosahedral with Fab

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    Component #1: virus, Human poliovirus 1 Mahoney

    VirusName: Human poliovirus 1 Mahoney / a.k.a: poliovirus 135S / Class: VIRION
    Details: native virus 160S is converted by heat-treatment to 135S
    Empty: No / Enveloped: No / Isolate: STRAIN
    SpeciesSpecies: Human poliovirus 1 Mahoney / virus / poliovirus 135S
    Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 20 mM Tris, 2 mM CaCl2 / pH: 7.5
    VitrificationInstrument: NONE / Cryogen name: ETHANE / Method: Blotted manually before plunging
    Details: Vitrification carried out in ambient atmosphere. Ethane cooled by liquid nitrogen.

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200FEG / Date: Jul 15, 1999
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 38000 X (nominal), 37752 X (calibrated) / Astigmatism: Bsoft / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 810 - 2240 nm
    Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
    Model: GATAN LIQUID NITROGEN
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 14 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8 / Details: Defocal pairs were used.

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 10160 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: Fourier Bessel / Software: EM3DR2 / CTF correction: CTF and decay correction of each particle
    Details: Reconstruction computed from focal pairs. Pairs not summed for reconstruction calculation.
    Resolution: 12 A / Resolution method: FSC 0.5

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