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    - PDB-3ezk: Bacteriophage T4 gp17 motor assembly based on crystal structures ... -

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    Basic information

    Entry
    Database: PDB / ID: 3ezk
    TitleBacteriophage T4 gp17 motor assembly based on crystal structures and cryo-EM reconstructions
    DescriptorDNA packaging protein Gp17
    KeywordsHYDROLASE / pentameric motor / DNA packaging / Alternative initiation / ATP-binding / DNA-binding / Hydrolase / Nuclease / Nucleotide-binding
    Specimen sourceBacteriophage T4 / virus
    MethodElectron microscopy (34 A resolution)
    AuthorsSun, S. / Rossmann, M.G.
    CitationCell, 2008, 135, 1251-1262

    Cell, 2008, 135, 1251-1262 StrPapers
    The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces.
    Siyang Sun / Kiran Kondabagil / Bonnie Draper / Tanfis I Alam / Valorie D Bowman / Zhihong Zhang / Shylaja Hegde / Andrei Fokine / Michael G Rossmann / Venigalla B Rao

    DateDeposition: Oct 23, 2008 / Release: Jan 13, 2009

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    Assembly

    Deposited unit
    A: DNA packaging protein Gp17
    B: DNA packaging protein Gp17
    C: DNA packaging protein Gp17
    D: DNA packaging protein Gp17
    E: DNA packaging protein Gp17

    331 kDa, 5 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    331,0245
    Polyers331,0245
    Non-polymers00
    Water0

    Omokage search
    #1idetical with deposited unit / defined by author / Symmetry operations: (identity)x1
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    Components

    #1polypeptide(L) / DNA packaging protein Gp17 / Terminase / Fragment: Residues 1-577 / Source: Bacteriophage T4 (gene. exp.) / References: UniProt: P17312

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY

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    Sample preparation

    Assembly of specimenName: T4 procapsid with gp17 bound / Aggregation state: PARTICLE
    Buffer solutionName: 50mM Tris-HCl, 100mM NaCl, 5mM MgCl2, 3mM beta-Mercaptoethanol
    Sample preparationpH: 7.4
    VitrificationDetails: flash-frozen on holey grids in liquid ethane

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    Electron microscopy imaging

    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: EMFIT
    3D reconstructionMethod: Spider / Resolution: 34 A / Nominal pixel size: 6.48 A/pix / Actual pixel size: 6.48 A/pix / CTF correction method: phase flipping of each micrograph
    Atomic model buildingMethod: N- and C-terminal domains were separately fitted into their corresponding cryoEM densities
    Software name: EMFIT / Ref protocol: Rigid body / Ref space: REAL / Target criteria: Sumf
    Number of atoms included #LASTProtein: 2765 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2765

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