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    ID:- Chain:- Residue:- Atom:-
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    Yorodumi
    - PDB-2y9j: THREE-DIMENSIONAL MODEL OF SALMONELLA'S NEEDLE COMPLEX AT SUBNANO... -

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    Basic information

    Entry
    Database: PDB / ID: 2y9j
    TitleTHREE-DIMENSIONAL MODEL OF SALMONELLA'S NEEDLE COMPLEX AT SUBNANOMETER RESOLUTION
    DescriptorPROTEIN PRGH
    LIPOPROTEIN PRGK
    KeywordsPROTEIN TRANSPORT / TYPE III SECRETION / IR1 / INNER MEMBRANE RING / C24-FOLD
    Specimen sourceSalmonella enterica subsp. enterica serovar typhimurium / bacteria
    Salmonella enterica subsp. enterica serovar tyhpimurium / bacteria
    MethodElectron microscopy (6.4 A resolution / Single particle / Vitreous ice)
    AuthorsSchraidt, O. / Marlovits, T.C.
    CitationScience, 2011, 331, 1192-1195

    Science, 2011, 331, 1192-1195 StrPapers
    Three-dimensional model of Salmonella's needle complex at subnanometer resolution.
    Oliver Schraidt / Thomas C Marlovits

    DateDeposition: Feb 15, 2011 / Release: Mar 23, 2011

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    Assembly

    Deposited unit
    A: PROTEIN PRGH
    B: PROTEIN PRGH
    C: PROTEIN PRGH
    D: PROTEIN PRGH
    E: PROTEIN PRGH
    F: PROTEIN PRGH
    G: PROTEIN PRGH
    H: PROTEIN PRGH
    I: PROTEIN PRGH
    J: PROTEIN PRGH
    K: PROTEIN PRGH
    L: PROTEIN PRGH
    M: PROTEIN PRGH
    N: PROTEIN PRGH
    O: PROTEIN PRGH
    P: PROTEIN PRGH
    Q: PROTEIN PRGH
    R: PROTEIN PRGH
    S: PROTEIN PRGH
    T: PROTEIN PRGH
    U: PROTEIN PRGH
    V: PROTEIN PRGH
    W: PROTEIN PRGH
    X: PROTEIN PRGH
    Y: LIPOPROTEIN PRGK
    Z: LIPOPROTEIN PRGK
    a: LIPOPROTEIN PRGK
    b: LIPOPROTEIN PRGK
    c: LIPOPROTEIN PRGK
    d: LIPOPROTEIN PRGK
    e: LIPOPROTEIN PRGK
    f: LIPOPROTEIN PRGK
    g: LIPOPROTEIN PRGK
    h: LIPOPROTEIN PRGK
    i: LIPOPROTEIN PRGK
    j: LIPOPROTEIN PRGK
    k: LIPOPROTEIN PRGK
    l: LIPOPROTEIN PRGK
    m: LIPOPROTEIN PRGK
    n: LIPOPROTEIN PRGK
    o: LIPOPROTEIN PRGK
    p: LIPOPROTEIN PRGK
    q: LIPOPROTEIN PRGK
    r: LIPOPROTEIN PRGK
    s: LIPOPROTEIN PRGK
    t: LIPOPROTEIN PRGK
    u: LIPOPROTEIN PRGK
    v: LIPOPROTEIN PRGK

    981 kDa, 48 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    980,53648
    Polyers980,53648
    Non-polymers00
    Water28,5361584

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

    #1polypeptide(L) / PROTEIN PRGH / Fragment: PERIPLASMIC DOMAIN, RESIDUES 177-362 / Source: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (gene. exp.) / References: UniProt: P41783
    #2polypeptide(L) / LIPOPROTEIN PRGK / PROTEIN PRGK / Fragment: PERIPLASMIC DOMAIN, RESIDUES 21-190 / Source: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYHPIMURIUM (gene. exp.) / References: UniProt: P41786
    #3ChemComp-HOH / water

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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: INNER MEMBRANE RING 1 / Aggregation state: PARTICLE
    Specimen supportDetails: CARBON
    VitrificationDetails: LIQUID ETHANE

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    Electron microscopy imaging

    MicroscopyMicroscope model: OTHER
    Details: MAGNIFICATION AT THE CCD 112969, CAMERA PIXEL 15UM, 1.33 ANGSTROM PER PIXEL, DATA COLLECTED SEMI- AUTOMATICALLY WITH POINT-2-POINT (DEVELOPED IN-HOUSE)
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: LOW DOSE
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 93000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
    CameraType: GATAN CCD 4KX4K
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: IMAGIC, CHIMERA
    3D reconstructionMethod: PROJECTION MATCHING / Resolution: 6.4 A / Actual pixel size: 1.33 A/pix / CTF correction method: EACH MICROGRAPH
    Details: RESOLUTION 6.4 ANGSTROM (0.5 FSC), 4.7 ANGSTROM (HALF BIT) PRGH (3GR1) MONOMERS WERE FITTED SEPARATELY, PRGK MODEL WAS BUILT BASED ON HOMOLOGY MODEL OF ESCJ (1YJ7) AND THEN INDIVIDUALLY FITTED INTO EM MAP. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1874. (DEPOSITION ID: 7821).
    Atomic model buildingMethod: CORRELATION / Ref space: REAL / Target criteria: CORRELATION
    Least-squares processHighest resolution: 6.4 A
    Refine hist #LASTHighest resolution: 6.4 A
    Number of atoms included #LASTProtein: 69120 / Nucleic acid: 0 / Ligand: 0 / Solvent: 1584 / Total: 70704

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