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    - PDB-3izg: Bacteriophage T7 prohead shell EM-derived atomic model -

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    Basic information

    Entry
    Database: PDB / ID: 3izg
    TitleBacteriophage T7 prohead shell EM-derived atomic model
    DescriptorMajor capsid protein 10A
    KeywordsVIRUS / bacteriophage / virus / capsid maturation / cryoelectron microscopy / morphogenetic intermediate / icosahedral
    Specimen sourceEnterobacteria phage T7 / virus / Bacteriophage T7
    MethodElectron microscopy (10.9 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsIonel, A. / Velazquez-Muriel, J.A. / Agirrezabala, X. / Luque, D. / Cuervo, A. / Caston, J.R. / Valpuesta, J.M. / Martin-Benito, J. / Carrascosa, J.L.
    CitationJ. Biol. Chem., 2011, 286, 234-242

    primary. J. Biol. Chem., 2011, 286, 234-242 StrPapers
    Molecular rearrangements involved in the capsid shell maturation of bacteriophage T7.
    Alina Ionel / Javier A Velázquez-Muriel / Daniel Luque / Ana Cuervo / José R Castón / José M Valpuesta / Jaime Martín-Benito / José L Carrascosa

    #1. Structure, 2007, 15, 461-472 StrPapers
    Quasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold.
    Agirrezabala, X. / Velazquez-Muriel, J.A. / Gomez-Puertas, P. / Scheres, S.H. / Carazo, J.M. / Carrascosa, J.L.

    DateDeposition: Oct 27, 2010 / Release: Nov 17, 2010 / Last modification: Feb 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
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    Assembly

    Deposited unit
    G: Major capsid protein 10A
    A: Major capsid protein 10A
    B: Major capsid protein 10A
    C: Major capsid protein 10A
    D: Major capsid protein 10A
    E: Major capsid protein 10A
    F: Major capsid protein 10A

    256 kDa, 7 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    256,1297
    Polyers256,1297
    Non-polymers00
    Water0

    Omokage search
    #1
    G: Major capsid protein 10A
    A: Major capsid protein 10A
    B: Major capsid protein 10A
    C: Major capsid protein 10A
    D: Major capsid protein 10A
    E: Major capsid protein 10A
    F: Major capsid protein 10A
    x 60
    complete icosahedral assembly / 15.4 MDa, 420 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    15,367,761420
    Polyers15,367,761420
    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
    G: Major capsid protein 10A
    A: Major capsid protein 10A
    B: Major capsid protein 10A
    C: Major capsid protein 10A
    D: Major capsid protein 10A
    E: Major capsid protein 10A
    F: Major capsid protein 10A
    x 5
    icosahedral pentamer / 1.28 MDa, 35 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,280,64735
    Polyers1,280,64735
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    G: Major capsid protein 10A
    A: Major capsid protein 10A
    B: Major capsid protein 10A
    C: Major capsid protein 10A
    D: Major capsid protein 10A
    E: Major capsid protein 10A
    F: Major capsid protein 10A
    x 6
    icosahedral 23 hexamer / 1.54 MDa, 42 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,536,77642
    Polyers1,536,77642
    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 10A / Source: Enterobacteria phage T7 (gene. exp.) / References: UniProt: P19726

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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: bacteriophage T7 prohead / Aggregation state: PARTICLE
    ComponentName: gp10A
    Details of the virusVirus host category: Bacteria / Virus host growth cell: Escherichia coli / Virus host species: Escherichia coli / Virus type: Prohead virion
    Buffer solutionName: 50mM Tris-HCl pH:7.7 10mM MgCl2 100mM NaCl
    Sample preparationpH: 7.7
    Specimen supportDetails: Quantifoil R2/2 carbon grids
    VitrificationCryogen name: ETHANE

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    Electron microscopy imaging

    MicroscopyMicroscope model: Tecnai G2
    Electron gunElectron source: Field Emission Gun / Accelerating voltage: 200 kV / Electron dose: 10 e/A2 / Illumination mode: SPOT SCAN
    Electron lensMode: Bright field / Nominal magnification: 50000 X / Calibrated magnification: 51600 X / Nominal defocus max: 1000 nm / Nominal defocus min: 3000 nm / Cs: 2.26 mm
    Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: KODAK SO163 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 reconstructionMethod: Spider / Software: Spider / Resolution: 10.9 A / Actual pixel size: 2.72 A/pix / CTF correction method: Wiener filter, defocus groups
    Number of atoms included #LASTProtein: 12831 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 12831

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