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    Yorodumi
    - PDB-2ob7: Structure of tmRNA-(SmpB)2 complex as inferred from cryo-EM -

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    Basic information

    Entry
    Database: PDB / ID: 2ob7
    TitleStructure of tmRNA-(SmpB)2 complex as inferred from cryo-EM
    DescriptorSsrA-binding protein/RNA Complex
    KeywordsRNA BINDING PROTEIN/RNA / tmRNA / SmpB / RNA BINDING PROTEIN-RNA COMPLEX
    Specimen sourceThermus thermophilus / bacteria / thermophilic
    MethodElectron microscopy (13.6 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsFrank, J. / Felden, B. / Gillet, R. / Li, W.
    CitationJ. Biol. Chem., 2007, 282, 6356-6363

    primary. J. Biol. Chem., 2007, 282, 6356-6363 StrPapers
    Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1.
    Reynald Gillet / Sukhjit Kaur / Wen Li / Marc Hallier / Brice Felden / Joachim Frank

    #1. Proc.Natl.Acad.Sci.USA, 2006, 103, 16484-16489
    Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome
    Kaur, S. / Gillet, R. / Li, W. / Gursky, R. / Frank, J.

    #2. Science, 2003, 300, 127-130
    Visualizing tmRNA entry into a stalled ribosome
    Valle, M. / Gillet, R. / Kaur, K. / Henne, A. / Ramakrishnan, V. / Frank, J.

    DateDeposition: Dec 18, 2006 / Release: Jan 23, 2007 / Last modification: Feb 24, 2009

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    Assembly

    Deposited unit
    A: transfer-messenger RNA
    D: 16S ribosomal RNA
    B: SsrA-binding protein
    C: SsrA-binding protein

    171 kDa, 4 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    170,5994
    Polyers170,5994
    Non-polymers00
    Water0

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

    #1RNA chain / transfer-messenger RNA / Source: Thermus thermophilus (gene. exp.)
    #2RNA chain / 16S ribosomal RNA / helix 44 of 30S ribosomal subunit / Source: Thermus thermophilus (gene. exp.)
    #3polypeptide(L) / SsrA-binding protein / Source: Thermus thermophilus (gene. exp.)

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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: Binding of transfer messenger RNA with two SmpBs / Aggregation state: PARTICLE
    Details: see Experimental Procedures in Kaur et al. (PNAS). [Deposition refers to structure of tmRNA-(SmpB)2 complex derived by fitting of EM map from Kaur et al. Fitting was modified in Gillet et al.]
    ComponentName: Pre-accommodated ribosomal trans-translation complex: T. thermophilus 70S-mRNA-(P-site tRNA)-tmRNA-(SmpB)2-(EF-Tu)-GDP-kirromycin
    Buffer solutionName: polimix
    Sample preparationpH: 7.5 / Sample conc.: 32 mg/ml
    Specimen supportDetails: This grid plus sample was kept at -80 degree C for several days before use.
    VitrificationDetails: Blot for 5 seconds before plunging. Rapid plunge freezing in liquid ethane.

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    Electron microscopy imaging

    MicroscopyMicroscope model: F20 / Date: Jun 1, 2004
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1500 e/A2 / Illumination mode: FLOOD BEAM LOW DOSE
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 55000 X / Calibrated magnification: 49000 X / Nominal defocus max: 3635 nm / Nominal defocus min: 1475 nm / Cs: 2 mm
    Specimen holderTemperature: 296 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    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

    Image selectionSoftware name: O
    EM single particle entitySymmetry type: ASYMMETRIC
    3D reconstructionMethod: single particle reconstruction / Resolution: 13.6 A / Nominal pixel size: 2.82 A/pix
    CTF correction method: CTF correction of each defocus group reconstruction, by Wiener filtering
    Atomic model buildingMethod: manual fitting using stereo visualization / Software name: O / Ref protocol: Manual / Ref space: REAL
    Number of atoms included #LASTProtein: 237 / Nucleic acid: 414 / Ligand: 0 / Solvent: 0 / Total: 651

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