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    Yorodumi
    - PDB-2xd8: Capsid structure of the infectious Prochlorococcus Cyanophage P-SSP7 -

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    Basic information

    Entry
    Database: PDB / ID: 2xd8
    TitleCapsid structure of the infectious Prochlorococcus Cyanophage P-SSP7
    DescriptorT7-LIKE CAPSID PROTEIN
    KeywordsVIRUS / MARINE PODOVIRUS / T7-LIKE VIRUS
    Specimen sourcePROCHLOROCOCCUS PHAGE P-SSP7 / virus
    MethodElectron microscopy (4.6 A resolution / Single particle / Vitreous ice)
    AuthorsLiu, X. / Zhang, Q. / Murata, K. / Baker, M.L. / Sullivan, M.B. / Fu, C. / Dougherty, M. / Schmid, M.F. / Osburne, M.S. / Chisholm, S.W. / Chiu, W.
    CitationNat. Struct. Mol. Biol., 2010, 17, 830-836

    Nat. Struct. Mol. Biol., 2010, 17, 830-836 StrPapers
    Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus.
    Xiangan Liu / Qinfen Zhang / Kazuyoshi Murata / Matthew L Baker / Matthew B Sullivan / Caroline Fu / Matthew T Dougherty / Michael F Schmid / Marcia S Osburne / Sallie W Chisholm / Wah Chiu

    DateDeposition: Apr 30, 2010 / Release: Jun 16, 2010 / Last modification: Mar 20, 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
    • EMDB-1713
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    Assembly

    Deposited unit
    A: T7-LIKE CAPSID PROTEIN
    B: T7-LIKE CAPSID PROTEIN
    C: T7-LIKE CAPSID PROTEIN
    D: T7-LIKE CAPSID PROTEIN
    E: T7-LIKE CAPSID PROTEIN
    F: T7-LIKE CAPSID PROTEIN
    G: T7-LIKE CAPSID PROTEIN

    276 kDa, 7 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    276,4627
    Polyers276,4627
    Non-polymers00
    Water0

    Omokage search
    #1
    A: T7-LIKE CAPSID PROTEIN
    B: T7-LIKE CAPSID PROTEIN
    C: T7-LIKE CAPSID PROTEIN
    D: T7-LIKE CAPSID PROTEIN
    E: T7-LIKE CAPSID PROTEIN
    F: T7-LIKE CAPSID PROTEIN
    G: T7-LIKE CAPSID PROTEIN
    x 60
    complete icosahedral assembly / 16.6 MDa, 420 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    16,587,724420
    Polyers16,587,724420
    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: T7-LIKE CAPSID PROTEIN
    B: T7-LIKE CAPSID PROTEIN
    C: T7-LIKE CAPSID PROTEIN
    D: T7-LIKE CAPSID PROTEIN
    E: T7-LIKE CAPSID PROTEIN
    F: T7-LIKE CAPSID PROTEIN
    G: T7-LIKE CAPSID PROTEIN
    x 5
    icosahedral pentamer / 1.38 MDa, 35 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,382,31035
    Polyers1,382,31035
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: T7-LIKE CAPSID PROTEIN
    B: T7-LIKE CAPSID PROTEIN
    C: T7-LIKE CAPSID PROTEIN
    D: T7-LIKE CAPSID PROTEIN
    E: T7-LIKE CAPSID PROTEIN
    F: T7-LIKE CAPSID PROTEIN
    G: T7-LIKE CAPSID PROTEIN
    x 6
    icosahedral 23 hexamer / 1.66 MDa, 42 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,658,77242
    Polyers1,658,77242
    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) / T7-LIKE CAPSID PROTEIN / GP10 / Source: PROCHLOROCOCCUS PHAGE P-SSP7 (gene. exp.) / References: UniProt: Q58N30

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    Experimental details

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    Experiment

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

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    Sample preparation

    Assembly of specimenName: CYANOPHAGE P-SSP7 / Aggregation state: PARTICLE
    Buffer solutionName: 100 MM TRIS-HCL, 100 MM MGSO4, AND 30 MM NACL
    Sample preparationpH: 7.5 / Sample conc.: 5 mg/ml
    Specimen supportDetails: HOLEY CARBON

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    Electron microscopy imaging

    MicroscopyMicroscope model: OTHER / Date: Aug 31, 2007
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: LOW DOSE
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 4.1 mm
    Specimen holderTemperature: 101 K
    CameraType: KODAK SO163 FILM
    EM image scansNumber digital images: 1059
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: MPSA / Number of particles: 36000
    3D reconstructionMethod: CROSS-COMMON LINES / Resolution: 4.6 A / Nominal pixel size: 1.27 A/pix / Actual pixel size: 1.17 A/pix / Magnification calibration: 2D CRYSTAL / CTF correction method: INDIVIDUAL MICROGRAPH
    Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1713.
    Least-squares processHighest resolution: 4.6 A
    Refine hist #LASTHighest resolution: 4.6 A
    Number of atoms included #LASTProtein: 2541 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2541

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