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    Yorodumi
    - PDB-3iys: Homology model of avian polyomavirus asymmetric unit -

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    Basic information

    Entry
    Database: PDB / ID: 3iys
    TitleHomology model of avian polyomavirus asymmetric unit
    DescriptorMajor capsid protein VP1
    KeywordsVIRUS / avian / polyomavirus / APV / icosahedral virus
    Specimen sourceBudgerigar fledgling disease polyomavirus / virus / BFPyV
    MethodElectron microscopy (11.3 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsShen, P.S. / Enderlein, D. / Nelson, C.D.S. / Carter, W.S. / Kawano, M. / Xing, L. / Swenson, R.D. / Olson, N.H. / Baker, T.S. / Cheng, R.H. / Atwood, W.J. / Johne, R. / Belnap, D.M.
    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 19, 2010 / Release: Jan 26, 2011 / Last modification: Mar 9, 2011

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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
    • EMDB-5180
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    Assembly

    Deposited unit
    A: Major capsid protein VP1
    B: Major capsid protein VP1
    C: Major capsid protein VP1
    D: Major capsid protein VP1
    E: Major capsid protein VP1
    F: Major capsid protein VP1

    225 kDa, 6 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    224,6986
    Polyers224,6986
    Non-polymers00
    Water0

    Omokage search
    #1
    A: Major capsid protein VP1
    B: Major capsid protein VP1
    C: Major capsid protein VP1
    D: Major capsid protein VP1
    E: Major capsid protein VP1
    F: Major capsid protein VP1
    x 60
    complete icosahedral assembly / 13.5 MDa, 360 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    13,481,893360
    Polyers13,481,893360
    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: Major capsid protein VP1
    B: Major capsid protein VP1
    C: Major capsid protein VP1
    D: Major capsid protein VP1
    E: Major capsid protein VP1
    F: Major capsid protein VP1
    x 5
    icosahedral pentamer / 1.12 MDa, 30 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,123,49130
    Polyers1,123,49130
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: Major capsid protein VP1
    B: Major capsid protein VP1
    C: Major capsid protein VP1
    D: Major capsid protein VP1
    E: Major capsid protein VP1
    F: Major capsid protein VP1
    x 6
    icosahedral 23 hexamer / 1.35 MDa, 36 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,348,18936
    Polyers1,348,18936
    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) / Major capsid protein VP1 / Major structural protein VP1 / Source: Budgerigar fledgling disease polyomavirus (gene. exp.) / References: UniProt: P13891

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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: avian polyomavirus / Aggregation state: PARTICLE / Details: Cryo-EM single particle reconstruction
    Details of the virusVirus host category: vertebrates / Virus host species: avian / Virus isolate: SPECIES / Virus type: virion
    Buffer solutionName: GP buffer with 250 mM L-arginine
    Sample preparationpH: 10.7
    Specimen supportDetails: avian polyomavirus in holey carbon grid
    VitrificationInstrument: FEI vitrobot / Cryogen name: ETHANE / Temp: 4 K / Humidity: 100% / Details: APV / Method: 3 second blot

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    Electron microscopy imaging

    EM imagingCamera length: 0 mm
    MicroscopyDate: Apr 23, 2007
    Electron gunAccelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 39000 X / Nominal defocus max: 4900 nm / Nominal defocus min: 500 nm
    Astigmatism: astigmatism was corrected at 59,000 times magnification
    Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
    Specimen holder type: Side entry liquid nitrogen-cooled cryo specimen holder
    Temperature: 90 K / Temperature (max): 95 K / Temperature (min): 88 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: UCSF Chimera
    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionMethod: Fourier Bessel / Software: PFT3DR / Resolution: 11.3 A / Number of particles: 5338 / Nominal pixel size: 1.63 A/pix / Actual pixel size: 1.57 A/pix
    Magnification calibration: against simian virus 40 atomic coordinates
    CTF correction method: full CTF correction (FSC cutoff 0.3) / Number of class averages: 0
    Atomic model buildingMethod: rigid body / Software name: UCSF Chimera / Ref protocol: rigid body / Ref space: REAL / Target criteria: cross-correlation coefficient
    Number of atoms included #LASTProtein: 2004 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2004

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