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    - EMDB-1553: Pretranslocation ribosome. Group after ML3D classification. Rache... -

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    Basic information

    Entry
    Database: EMDB / ID: 1553
    TitlePretranslocation ribosome. Group after ML3D classification. Racheted ribosome with tRNAs in hybrid positions.
    Keywordsribosome / pretranslocation / hybrid
    Sample70 mRNA tRNAfMet fMetLeu-tRNALeu
    SourceEscherichia coli / bacteria /
    Map dataRacheted ribosome with tRNAs in hybrid positions.
    Methodsingle particle reconstruction, at 16 A resolution
    AuthorsJulian P / Konevega AL / Scheres SHW / Lazaro M / Gil D / Wintermeyer W / Rodnina MV / Valle M
    CitationProc. Natl. Acad. Sci. U.S.A., 2008, 105, 16924-16927

    Proc. Natl. Acad. Sci. U.S.A., 2008, 105, 16924-16927 StrPapers
    Structure of ratcheted ribosomes with tRNAs in hybrid states.
    Patricia Julián / Andrey L Konevega / Sjors H W Scheres / Melisa Lázaro / David Gil / Wolfgang Wintermeyer / Marina V Rodnina / Mikel Valle

    DateDeposition: Sep 8, 2008 / Header (metadata) release: Sep 15, 2008 / Map release: May 5, 2009 / Last update: Sep 8, 2008

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 32
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 32
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1553.map.gz (map file in CCP4 format, 16001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    160 pix
    2.2 A/pix
    = 352. A
    160 pix
    2.2 A/pix
    = 352. A
    160 pix
    2.2 A/pix
    = 352. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.2 A
    Density
    Contour Level:32 (by author), 32 (movie #1):
    Minimum - Maximum-81.066 - 192.719
    Average (Standard dev.)3.9672 (24.5844)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions160160160
    Origin-80-80-80
    Limit797979
    Spacing160160160
    CellA=B=C: 352 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.22.22.2
    M x/y/z160160160
    origin x/y/z0.0000.0000.000
    length x/y/z352.000352.000352.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-81-81-81
    NX/NY/NZ160160160
    MAP C/R/S123
    start NC/NR/NS-80-80-80
    NC/NR/NS160160160
    D min/max/mean-81.066192.7193.967

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    Supplemental data

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    Sample components

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    Entire 70 mRNA tRNAfMet fMetLeu-tRNALeu

    EntireName: 70 mRNA tRNAfMet fMetLeu-tRNALeu / Number of components: 3

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    Component #1: ribosome-prokaryote, 70S E.coli ribosome in the pretranslocation state

    Ribosome-prokaryoteName: 70S E.coli ribosome in the pretranslocation state / a.k.a: pretranslocation ribosome / Prokaryote: ALL / Recombinant expression: No
    SourceSpecies: Escherichia coli / bacteria /

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 50 mM Tris-HCl, pH 7.5 30mM KCl 70 mM NH4Cl 20 mM MgCl2 2 mM spermine
    pH: 7.5
    Support filmQuantifoil 300 mesh copper
    StainingcryoEM
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 100 % / Method: single blot for 1.5 seconds / Details: Vitrification instrument: Vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 2200FS
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
    LensCs: 2 mm / Imaging mode: BRIGHT FIELD
    Specimen HolderHolder: single tilt cryoholder / Model: GATAN LIQUID NITROGEN / Temperature: 90 K
    CameraDetector: GENERIC GATAN

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    Image acquisition

    Image acquisitionSampling size: 2.2 microns

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 12590 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: reference matching / Software: SPIDER XMIPP / CTF correction: volume / Details: subset after ML3D classification / Resolution: 16 A / Resolution method: FSC at 0.15 cut-off

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