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    - PDB-2noq: Structure of ribosome-bound cricket paralysis virus IRES RNA -

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    Basic information

    Entry
    Database: PDB / ID: 2noq
    TitleStructure of ribosome-bound cricket paralysis virus IRES RNA
    DescriptorRibosome
    KeywordsRIBOSOME / IRES RNA / Ribosome / Translation / Internal Initiation
    Specimen sourceSaccharomyces cerevisiae / yeast / baker's yeast /
    MethodElectron microscopy (7.3 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsSchuler, M. / Connell, S.R. / Lescoute, A. / Giesebrecht, J. / Dabrowski, M. / Schroeer, B. / Mielke, T. / Penczek, P.A. / Westhof, E. / Spahn, C.M.T.
    CitationNat. Struct. Mol. Biol., 2006, 13, 1092-1096

    Nat. Struct. Mol. Biol., 2006, 13, 1092-1096 StrPapers
    Structure of the ribosome-bound cricket paralysis virus IRES RNA.
    Martin Schüler / Sean R Connell / Aurelie Lescoute / Jan Giesebrecht / Marylena Dabrowski / Birgit Schroeer / Thorsten Mielke / Pawel A Penczek / Eric Westhof / Christian M T Spahn

    DateDeposition: Oct 26, 2006 / Release: Nov 21, 2006 / Last modification: Feb 15, 2012

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    Assembly

    Deposited unit
    A: CrPV IRES
    B: 18S ribosomal RNA
    C: 18S ribosomal RNA
    D: 18S ribosomal RNA
    E: 25S ribosomal RNA
    F: 40S ribosomal protein S5
    G: 60S ribosomal protein L1
    H: 60S ribosomal protein L11-B

    161 kDa, 8 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    161,1928
    Polyers161,1928
    Non-polymers00
    Water0

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

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    RNA chain , 5 types, 5 molecules ABCDE

    #1RNA chain / CrPV IRES / References: GenBank: 8895506
    #2RNA chain / 18S ribosomal RNA / Fragment: residues 500-545 / Source: Saccharomyces cerevisiae (gene. exp.)
    #3RNA chain / 18S ribosomal RNA / Fragment: residues 1050-1062 / Source: Saccharomyces cerevisiae (gene. exp.)
    #4RNA chain / 18S ribosomal RNA / Fragment: residues 1194-1208 / Source: Saccharomyces cerevisiae (gene. exp.)
    #5RNA chain / 25S ribosomal RNA / S2, YS8, RP14 / Source: Saccharomyces cerevisiae (gene. exp.)

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    40S ribosomal protein ... , 1 types, 1 molecules F

    #6polypeptide(L) / 40S ribosomal protein S5 / L10a / Source: Saccharomyces cerevisiae (gene. exp.) / References: UniProt: P26783

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    60S ribosomal protein ... , 2 types, 2 molecules GH

    #7polypeptide(L) / 60S ribosomal protein L1 / L16, YL16, 39B, RP39 / Source: Saccharomyces cerevisiae (gene. exp.) / References: UniProt: P53030
    #8polypeptide(L) / 60S ribosomal protein L11-B / Source: Saccharomyces cerevisiae (gene. exp.) / References: UniProt: Q3E757

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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 specimenName: Yeast 80S bound by cricket paralysis virus IRES RNA / Aggregation state: PARTICLE
    Buffer solutionName: 20 mM Hepes pH 7.6, 100 mM KAc, 100 mM KCl, 5 mM MgCl2, 1 mM DTT, 1mM AEBSF, Roche Complete Protease Inhibitor
    Specimen supportDetails: Quantifoil

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI-POLARA G2
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV
    Electron lensNominal magnification: 39000 X / Nominal defocus max: 3900 nm / Nominal defocus min: 100 nm
    CameraType: KODAK SO163 FILM
    DetectorType: 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

    EM single particle entitySymmetry type: ASYMMETRIC
    3D reconstructionMethod: Iterative 3D-Projection Matching / Resolution: 7.3 A / Nominal pixel size: 1.22 A/pix
    Number of atoms included #LASTProtein: 4163 / Nucleic acid: 6746 / Ligand: 0 / Solvent: 0 / Total: 10909

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