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    - PDB-3cnf: 3.88 Angstrom structure of cytoplasmic polyhedrosis virus by cryo... -

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    Basic information

    Entry
    Database: PDB / ID: 3cnf
    Title3.88 Angstrom structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy
    DescriptorVP1, VP3
    KeywordsVIRUS / cytoplasmic polyhedrosis virus / capsid protein / turret protein / polyhedrin-binding domain / guanylyltransferase domain / icosahedral virus
    Specimen sourceBombyx mori cypovirus 1 / virus / image: Bombyx mori
    MethodElectron microscopy (3.88 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsYu, X. / Jin, L. / Zhou, Z.H.
    CitationNature, 2008, 453, 415-419

    Nature, 2008, 453, 415-419 StrPapers
    3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy.
    Xuekui Yu / Lei Jin / Z Hong Zhou

    DateDeposition: Mar 25, 2008 / Release: Apr 29, 2008 / Last modification: Feb 24, 2009

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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-1508
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    Assembly

    Deposited unit
    A: VP1
    B: VP1
    T: VP3

    417 kDa, 3 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    416,8713
    Polyers416,8713
    Non-polymers00
    Water0

    Omokage search
    #1
    A: VP1
    B: VP1
    T: VP3
    x 60
    complete icosahedral assembly / 25 MDa, 180 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    25,012,275180
    Polyers25,012,275180
    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: VP1
    B: VP1
    T: VP3
    x 5
    icosahedral pentamer / 2.08 MDa, 15 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    2,084,35615
    Polyers2,084,35615
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: VP1
    B: VP1
    T: VP3
    x 6
    icosahedral 23 hexamer / 2.5 MDa, 18 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    2,501,22818
    Polyers2,501,22818
    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) / VP1 / Source: Bombyx mori cypovirus 1 (gene. exp.) / References: UniProt: Q6TS43
    #2polypeptide(L) / VP3 / Source: Bombyx mori cypovirus 1 (gene. exp.) / References: UniProt: Q9E957

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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: CYTOPLASMIC POLYHEDROSIS VIRUS / Aggregation state: PARTICLE
    Details of the virusVirus host category: insect cells / Virus host species: Bombyx mori / Virus isolate: STRAIN / Virus type: virion
    Buffer solutionName: 10MM PBS
    Sample preparationpH: 7.4 / Sample conc.: 3 mg/ml
    Specimen supportDetails: THE VIRIONS WERE EMBEDDED IN A THIN LAYER OF VITREOUS ICE SUSPENDED ACROSS THE HOLES OF HOLEY CARBON FILMS FOR CRYOEM IMAGING.
    VitrificationDetails: PLUNGED INTO LIQUID ETHANE

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI POLARA
    Details: SAMPLES WERE MAINTAINED AT 100K IN THE ELECTRON MICROSCOPE.
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/A2 / Illumination mode: LOW DOSE
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 154380 X / Calibrated magnification: 154380 X / Nominal defocus max: 13 nm / Nominal defocus min: 15 nm / Cs: 2 mm
    Specimen holderTemperature: 1 K
    CameraType: TVIPS CCD
    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionNumber of particles: 12814
    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionMethod: FOURIER COMMON LINES AND FOURIER- BESSEL SYNTHESIS / Resolution: 3.88 A / Nominal pixel size: 0.972 A/pix / Actual pixel size: 0.972 A/pix / CTF correction method: CTF CORRECTION OF EACH PARTICLE
    Details: PRIOR TO THE MERGING OF PARTICLES FOR 3D RECONSTRUCTION, THE FOURIER TRANSFORM VALUES OF INDIVIDUAL IMAGES WERE CORRECTED FOR THE CTF.
    Least-squares processHighest resolution: 3.88 A
    Refine hist #LASTHighest resolution: 3.88 A
    Number of atoms included #LASTProtein: 2199 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2199

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