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    - PDB-2om7: Structural Basis for Interaction of the Ribosome with the Switch ... -

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    Basic information

    Entry
    Database: PDB / ID: 2om7
    TitleStructural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors
    DescriptorRNA binding protein/RNA Complex
    KeywordsRIBOSOME / RNA-Protein Complex
    Specimen sourceThermus thermophilus / bacteria / thermophilic
    MethodElectron microscopy (7.3 A resolution)
    AuthorsConnell, S.R. / Wilson, D.N. / Rost, M. / Schueler, M. / Giesebrecht, J. / Dabrowski, M. / Mielke, T. / Fucini, P. / Spahn, C.M.T.
    CitationMol. Cell, 2007, 25, 751-764

    Mol. Cell, 2007, 25, 751-764 StrPapers
    Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
    Sean R Connell / Chie Takemoto / Daniel N Wilson / Hongfei Wang / Kazutaka Murayama / Takaho Terada / Mikako Shirouzu / Maximilian Rost / Martin Schüler / Jan Giesebrecht / Marylena Dabrowski / Thorsten Mielke / Paola Fucini / Shigeyuki Yokoyama / Christian M T Spahn

    DateDeposition: Jan 21, 2007 / Release: Jan 15, 2008 / Last modification: Mar 12, 2014

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    Assembly

    Deposited unit
    A: Fragment of 16S rRNA (h14)
    B: Fragment of 16S rRNA (h15)
    C: Fragment of 16S rRNA (h44)
    D: 16S ribosomal RNA (H5)
    F: Fragment of23S rRNA (H95)
    G: Fragment of23S rRNA (H68)
    H: Fragment of23S rRNA (H89)
    I: Fragment of23S rRNA (H42-44)
    J: Fragment of23S rRNA (H76)
    M: p/E-tRNA
    E: 30S ribosomal protein S12
    K: 50S ribosomal protein L1
    L: Elongation factor G
    N: 30S ribosomal protein S2

    405 kDa, 14 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    404,60514
    Polyers404,60514
    Non-polymers00
    Water0

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

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    RNA chain , 10 types, 10 molecules ABCDFGHIJM

    #1RNA chain / Fragment of 16S rRNA (h14) / Source: Thermus thermophilus (gene. exp.)
    #2RNA chain / Fragment of 16S rRNA (h15) / Source: Thermus thermophilus (gene. exp.)
    #3RNA chain / Fragment of 16S rRNA (h44) / Source: Thermus thermophilus (gene. exp.) / References: GenBank: 118505352
    #4RNA chain / 16S ribosomal RNA (H5) / Source: Thermus thermophilus (gene. exp.) / References: GenBank: 48256
    #5RNA chain / Fragment of23S rRNA (H95) / Source: Thermus thermophilus (gene. exp.)
    #6RNA chain / Fragment of23S rRNA (H68) / Source: Thermus thermophilus (gene. exp.) / References: GenBank: 37223182
    #7RNA chain / Fragment of23S rRNA (H89) / Source: Thermus thermophilus (gene. exp.)
    #8RNA chain / Fragment of23S rRNA (H42-44) / Source: Thermus thermophilus (gene. exp.) / References: GenBank: 37223182
    #9RNA chain / Fragment of23S rRNA (H76) / Source: Thermus thermophilus (gene. exp.) / References: GenBank: 37223182
    #10RNA chain / p/E-tRNA / Source: Thermus thermophilus (gene. exp.)

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    30S ribosomal protein ... , 2 types, 2 molecules EN

    #11polypeptide(L) / 30S ribosomal protein S12 / Source: Thermus thermophilus (gene. exp.) / References: UniProt: P17293
    #14polypeptide(L) / 30S ribosomal protein S2 / Source: Thermus thermophilus (gene. exp.) / References: UniProt: P80371

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    50S ribosomal protein ... / polypeptide(L) , 2 types, 2 molecules KL

    #12polypeptide(L) / 50S ribosomal protein L1 / Source: Thermus thermophilus (gene. exp.) / References: UniProt: Q5SLP7
    #13polypeptide(L) / Elongation factor G / EF-G / Source: Thermus thermophilus (gene. exp.) / References: UniProt: P13551

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY

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    Sample preparation

    Assembly of specimenName: complex of Thermus thermophilus 70S ribosomes and EF-G-GMPPNP
    Aggregation state: PARTICLE
    Component
    NameAssembly idIDGo idIpr id
    30S ribosomal protein S12110015935005679
    50S ribosomal protein L1120006412002143
    Elongation factor G130006414004540
    30S ribosomal protein S2140003735001865
    Buffer solutionName: 0.3 mM GMPPNP, 10 mM Hepes-KOH (pH 7.8), 10 mM Mg acetate, 60 mM NH4Cl, and 6 mM B-mercaptoethanol
    Sample preparationpH: 7.8
    VitrificationInstrument: Vitrobot / Cryogen name: ETHANE / Temp: 277 K / Humidity: 95

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI TECNAI F30
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 19 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 800 nm
    Specimen holderSpecimen holder type: Eucentric
    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

    SoftwareName: SPIDER / Classification: refinement
    Image selectionSoftware name: SPIDER
    3D reconstructionResolution: 7.3 A / CTF correction method: defocus groups
    Details: The geometry of linkages between some residues in chains J, M and L are distorted. They were not resolved based on the data used for solving this structure.
    Atomic model buildingMethod: Rigid Body / Software name: Situs
    Number of atoms included #LASTProtein: 9140 / Nucleic acid: 9891 / Ligand: 0 / Solvent: 0 / Total: 19031

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