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    - PDB-3iym: Backbone Trace of the Capsid Protein Dimer of a Fungal Partitivir... -

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    Basic information

    Entry
    Database: PDB / ID: 3iym
    TitleBackbone Trace of the Capsid Protein Dimer of a Fungal Partitivirus from Electron Cryomicroscopy and Homology Modeling
    DescriptorCapsid protein
    KeywordsVIRUS / dsRNA virus / icosahedral virus / partitivirus / Penicillium stoloniferum virus S / PsV-S
    Specimen sourcePenicillium stoloniferum virus S / virus
    MethodElectron microscopy (4.7 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsTang, J. / Pan, J. / Havens, W.F. / Ochoa, W.F. / Li, H. / Sinkovits, R.S. / Guu, T.S.Y. / Ghabrial, S.A. / Nibert, M.L. / Tao, J.Y. / Baker, T.S.
    CitationBiophys. J., 2010, 99, 685-694

    Biophys. J., 2010, 99, 685-694 StrPapers
    Backbone trace of partitivirus capsid protein from electron cryomicroscopy and homology modeling.
    Jinghua Tang / Junhua Pan / Wendy M Havens / Wendy F Ochoa / Tom S Y Guu / Said A Ghabrial / Max L Nibert / Yizhi Jane Tao / Timothy S Baker

    DateDeposition: Feb 5, 2010 / Release: Jul 28, 2010 / Last modification: Nov 13, 2013

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    Structure visualization

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    • Biological unit as complete icosahedral assembly
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    • Biological unit as icosahedral pentamer
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    • Biological unit as icosahedral 23 hexamer
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    • Deposited structure unit
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    • Simplified surface model + fitted atomic model
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    • Simplified surface model + fitted atomic model
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    Assembly

    Deposited unit
    A: Capsid protein
    B: Capsid protein

    93.7 kDa, 2 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    93,6622
    Polyers93,6622
    Non-polymers00
    Water0

    Omokage search
    #1
    A: Capsid protein
    B: Capsid protein
    x 60
    complete icosahedral assembly / 5.62 MDa, 120 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    5,619,722120
    Polyers5,619,722120
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x60
    Download / Omokage search
    #2idetical with deposited unit in distinct coordinate / icosahedral asymmetric unit / Symmetry operations: (point symmetry)x1
    #3
    A: Capsid protein
    B: Capsid protein
    x 5
    icosahedral pentamer / 468 kDa, 10 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    468,31010
    Polyers468,31010
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: Capsid protein
    B: Capsid protein
    x 6
    icosahedral 23 hexamer / 562 kDa, 12 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    561,97212
    Polyers561,97212
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x6
    PAUidetical with deposited unit in distinct coordinate / icosahedral asymmetric unit, std point frame / Symmetry operations: (transform to point frame)x1

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    Components

    #1polypeptide(L) / Capsid protein / Source: Penicillium stoloniferum virus S (gene. exp.) / References: UniProt: Q6YDQ6

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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    Sample preparation

    Assembly of specimenName: PsV-S / Aggregation state: PARTICLE / Number of components: 1
    ComponentName: PsV-S / Details: authentic virus particles / Type: VIRUS
    Details of the virusEmpty: NO / Enveloped: NO / Virus host category: FUNGI / Virus host growth cell: Penicillium stoloniferum / Virus host species: Fungi / Virus isolate: SPECIES / Virus type: VIRION
    Buffer solutionName: 50mM Tris pH7.6, 150mM NaCl, 5mM EDTA, 1mM DTT
    Sample preparationpH: 7.6 / Sample conc.: 5 mg/ml
    VitrificationCryogen name: ETHANE / Temp: 89 K / Humidity: 80 / Method: blot for 7.5 seconds before plunging

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    Electron microscopy imaging

    EM imagingCamera length: 0 mm
    MicroscopyMicroscope model: TECNAI G2
    Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2.2 nm / Nominal defocus min: 1.4 nm
    Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Eucentric / Temperature: 77 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: KODAK SO-163 electron-image FILM
    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

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    Processing

    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionSoftware: AUTO3DEM / Resolution: 4.7 A / Number of particles: 14252 / Nominal pixel size: 1.27 A/pix / Actual pixel size: 1.27 A/pix
    Number of atoms included #LASTProtein: 3168 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 3168

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