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    - PDB-1pn7: Coordinates of S12, L11 proteins and P-tRNA, from the 70S X-ray s... -

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    Basic information

    Entry
    Database: PDB / ID: 1pn7
    TitleCoordinates of S12, L11 proteins and P-tRNA, from the 70S X-ray structure aligned to the 70S Cryo-EM map of E.coli ribosome
    DescriptorRNA BINDING PROTEIN/RNA Complex
    KeywordsRNA binding protein/RNA / ribosomal protein / tRNA binding protein / tRNA / RNA binding protein-RNA COMPLEX
    Specimen sourceThermus thermophilus / bacteria / thermophilic
    Thermotoga maritima / bacteria / thermophilic
    MethodElectron microscopy (10.8 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsValle, M. / Zavialov, A. / Sengupta, J. / Rawat, U. / Ehrenberg, M. / Frank, J.
    CitationCell, 2003, 114, 123-134

    Cell, 2003, 114, 123-134 StrPapers
    Locking and unlocking of ribosomal motions.
    Mikel Valle / Andrey Zavialov / Jayati Sengupta / Urmila Rawat / Måns Ehrenberg / Joachim Frank

    DateDeposition: Jun 12, 2003 / Release: Jul 15, 2003 / Last modification: Feb 2, 2010

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    Assembly

    Deposited unit
    C: P-tRNA
    O: 30S ribosomal protein S12
    L: 50S ribosomal protein L11

    48.1 kDa, 3 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    48,1173
    Polyers48,1173
    Non-polymers00
    Water0

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

    #1RNA chain / P-tRNA
    #2polypeptide(L) / 30S ribosomal protein S12 / Source: Thermus thermophilus (gene. exp.) / References: UniProt: Q5SHN3
    #3polypeptide(L) / 50S ribosomal protein L11 / Source: Thermotoga maritima (gene. exp.) / References: UniProt: P29395

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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
    Component
    NameAssembly idIDGo idIpr id
    P-tRNA11
    30S ribosomal protein S12120006412006032
    50S ribosomal protein L11130006412000911
    Sample preparationpH: 7.5 / Sample conc.: 32 mg/ml
    Specimen supportDetails: Quantifoil holley-carbon film grids
    VitrificationDetails: Rapid-freezing in liquid ethane

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI TECNAI F20 / Date: Jun 1, 2001
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2000 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 49696 X / Nominal defocus max: 4 nm / Nominal defocus min: 15 nm / Cs: 2 mm
    Specimen holderTemperature: 93 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: KODAK SO163 FILM

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    Processing

    EM single particle entitySymmetry type: ASYMMETRIC
    3D reconstructionMethod: 3D projection matching; conjugate gradients with regularization
    Resolution: 10.8 A / Actual pixel size: 2.82 A/pix / Magnification calibration: TMV
    CTF correction method: CTF correction of 3D-maps by Wiener filtration
    Details: SPIDER package. Crystal Structure of Thermus Thermophilus 70S ribosome
    Atomic model buildingMethod: Manual fitting in O / Ref space: REAL
    Number of atoms included #LASTProtein: 257 / Nucleic acid: 62 / Ligand: 0 / Solvent: 0 / Total: 319

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