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    Yorodumi
    - PDB-3h3w: Fitting of the gp6 crystal structure into 3D cryo-EM reconstructi... -

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    Basic information

    Entry
    Database: PDB / ID: 3h3w
    TitleFitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 dome-shaped baseplate
    DescriptorBaseplate structural protein Gp6
    KeywordsVIRAL PROTEIN / viral structural protein / Virion
    Specimen sourceEnterobacteria phage T4 / virus / Bacteriophage T4
    MethodElectron microscopy (12 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsAksyuk, A.A. / Leiman, P.G. / Shneider, M.M. / Mesyanzhinov, V.V. / Rossmann, M.G.
    CitationStructure, 2009, 17, 800-808

    Structure, 2009, 17, 800-808 StrPapers
    The structure of gene product 6 of bacteriophage T4, the hinge-pin of the baseplate.
    Anastasia A Aksyuk / Petr G Leiman / Mikhail M Shneider / Vadim V Mesyanzhinov / Michael G Rossmann

    DateDeposition: Apr 17, 2009 / Release: May 19, 2009 / Last modification: Jan 19, 2010

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    Assembly

    Deposited unit
    A: Baseplate structural protein Gp6
    B: Baseplate structural protein Gp6
    C: Baseplate structural protein Gp6
    D: Baseplate structural protein Gp6
    E: Baseplate structural protein Gp6
    F: Baseplate structural protein Gp6
    G: Baseplate structural protein Gp6
    H: Baseplate structural protein Gp6
    I: Baseplate structural protein Gp6
    J: Baseplate structural protein Gp6
    K: Baseplate structural protein Gp6
    L: Baseplate structural protein Gp6

    460 kDa, 12 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    459,65912
    Polyers459,65912
    Non-polymers00
    Water0

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

    #1polypeptide(L) / Baseplate structural protein Gp6 / Baseplate wedge protein 6 / Fragment: gene product 6 deletion fragment / Mutation: residues 334-660 / Source: Enterobacteria phage T4 (gene. exp.) / References: UniProt: P19060

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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 specimenAggregation state: PARTICLE
    ComponentName: ring of 12 molecules of gene product 6
    Details: assembly of gp6 in the dome-shaped baseplate of bacteriophage T4
    Sample preparationpH: 7 / Sample conc.: 5 mg/ml

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T / Date: Jan 30, 2001
    Electron gunElectron source: FIELD EMISSION GUN / Electron dose: 25 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensNominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
    Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: 626 Single Tilt Cryotransfer System
    Radiation wavelengthRelative weight: 1
    ReflectionD resolution high: 12 A

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    Processing

    Image selectionSoftware name: COLORES from the SITUS program package was used for the fitting
    EM single particle entitySymmetry type: CYCLIC
    Atomic model buildingSoftware name: COLORES from the SITUS program package was used for the fitting
    Ref space: REAL
    Least-squares processHighest resolution: 12 A
    Refine hist #LASTHighest resolution: 12 A
    Number of atoms included #LASTProtein: 31380 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 31380

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