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    - EMDB-1311: Cryo-EM visualization of transfer messenger RNA with two SmpBs in... -

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    Basic information

    Entry
    Database: EMDB / ID: 1311
    TitleCryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome.
    SampleThermus thermophilus 70S ribosome
    SourceThermus thermophilus / bacteria / thermophilic / tRNA
    Map dataCryo-EM map of Thermus thermophilus 70S ribosome bound with tmRNA, two small protein B, and EF-Tu in the presence of S1 in solution.
    Methodsingle particle reconstruction, at 13.6 A resolution
    AuthorsKaur S / Gillet R / Li W / Gursky R / Frank J
    CitationProc. Natl. Acad. Sci. U.S.A., 2006, 103, 16484-16489

    Proc. Natl. Acad. Sci. U.S.A., 2006, 103, 16484-16489 StrPapers
    Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome.
    Sukhjit Kaur / Reynald Gillet / Wen Li / Richard Gursky / Joachim Frank

    DateDeposition: Dec 13, 2006 / Header (metadata) release: Dec 14, 2006 / Map release: Dec 14, 2006 / Last update: Dec 13, 2006

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 30.915807559
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by height
    • Surface level: 30.915807559
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1311.map.gz (map file in CCP4 format, 8584 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    130 pix
    2.82 A/pix
    = 366.6 A
    130 pix
    2.82 A/pix
    = 366.6 A
    130 pix
    2.82 A/pix
    = 366.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.82 A
    Density
    Contour Level:73.2, 30.9158076 (movie #1):
    Minimum - Maximum-117.854 - 304.088
    Average (Standard dev.)6.06499 (30.402)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions130130130
    Origin-65-65-65
    Limit646464
    Spacing130130130
    CellA=B=C: 366.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.822.822.82
    M x/y/z130130130
    origin x/y/z0.0000.0000.000
    length x/y/z366.600366.600366.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-63-63-63
    NX/NY/NZ128128128
    MAP C/R/S123
    start NC/NR/NS-65-65-65
    NC/NR/NS130130130
    D min/max/mean-117.854304.0886.065

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    Supplemental data

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    Sample components

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    Entire Thermus thermophilus 70S ribosome

    EntireName: Thermus thermophilus 70S ribosome / Number of components: 5
    MassTheoretical: 2.4 MDa

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    Component #1: ribosome-prokaryote, 70S Ribosome

    Ribosome-prokaryoteName: 70S Ribosome / Prokaryote: ALL
    MassExperimental: 2.3 MDa

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    Component #2: protein, small protein B

    ProteinName: small protein B / Recombinant expression: No / Number of Copies: 2
    MassExperimental: 19 kDa
    SourceSpecies: Thermus thermophilus / bacteria / thermophilic

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    Component #3: nucleic-acid, tmRNA

    Nucleic-acidName: tmRNA / Class: RNA / Structure: OTHER / Synthetic: No
    SourceSpecies: Thermus thermophilus / bacteria / thermophilic

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    Component #4: nucleic-acid, tRNA

    Nucleic-acidName: tRNA / Class: T-RNA / Structure: OTHER / Synthetic: No
    SourceSpecies: Thermus thermophilus / bacteria / thermophilic / tRNA

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    Component #5: protein, EF-Tu

    ProteinName: EF-Tu / Number of Copies: 1 / Recombinant expression: No
    SourceSpecies: Thermus thermophilus / bacteria / thermophilic

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: see Methods / pH: 7.5
    Support filmQuanti-foil grids coated with a thin carbon layer
    StainingNo staining (Cryo-EM)
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 279 K / Humidity: 80 %
    Method: Blot for 5 seconds before plunging Rapid plunge freezing in liquid ethane
    Details: Vitrification instrument: Vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20 / Date: Aug 13, 2004
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
    LensMagnification: 5000 X (nominal), 49696 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1475 - 3635 nm
    Specimen HolderHolder: cryo transfer / Model: GATAN LIQUID NITROGEN / Temperature: 93 K ( 93 - 93 K)
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 27 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 52829 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Back projection / Software: SPIDER package / CTF correction: CTF correctionn of 3D map / Resolution: 13.6 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: O / Refinement protocol: rigid body / Details: Protocol: Rigid Body. manual fitting with O

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