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    Yorodumi
    - EMDB-5267: Intermediate states observed in the pre-translocation ribosome du... -

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    Basic information

    Entry
    Database: EMDB / ID: 5267
    TitleIntermediate states observed in the pre-translocation ribosome during tRNA translocation
    Keywordsribosome / translocation / tRNA
    Samplepre-translocation ribosome complex
    SourceEscherichia coli / bacteria /
    Map dataE. coli ribosome: intermediate rotated structure 2
    Methodsingle particle reconstruction, at 13.2 A resolution
    AuthorsFu J / Munro J / Blanchard SC / Frank J
    CitationProc. Natl. Acad. Sci. U.S.A., 2011, 108, 4817-4821

    Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 4817-4821 StrPapers
    Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation.
    Jie Fu / James B Munro / Scott C Blanchard / Joachim Frank

    DateDeposition: Feb 25, 2011 / Header (metadata) release: Feb 28, 2011 / Map release: Feb 28, 2011 / Last update: Feb 25, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 50
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 50
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_5267.map.gz (map file in CCP4 format, 7631 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    125 pix
    3 A/pix
    = 375. A
    125 pix
    3 A/pix
    = 375. A
    125 pix
    3 A/pix
    = 375. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 3 A
    Density
    Contour Level:50 (by author), 50 (movie #1):
    Minimum - Maximum-85.94808197 - 214.2815094
    Average (Standard dev.)5.23832273 (24.46959686)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions125125125
    Origin-62-62-62
    Limit626262
    Spacing125125125
    CellA=B=C: 375 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z333
    M x/y/z125125125
    origin x/y/z0.0000.0000.000
    length x/y/z375.000375.000375.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-62-62-62
    NC/NR/NS125125125
    D min/max/mean-85.948214.2825.238

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    Supplemental data

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    Sample components

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    Entire pre-translocation ribosome complex

    EntireName: pre-translocation ribosome complex / Number of components: 3
    MassTheoretical: 2.5 MDa

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    Component #1: ribosome-prokaryote, ribosome

    Ribosome-prokaryoteName: ribosome / Prokaryote: ALL / Recombinant expression: No
    MassTheoretical: 2.5 MDa
    SourceSpecies: Escherichia coli / bacteria /

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Method: blot for 8 seconds / Details: Vitrification instrument: vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: FEI POLARA 300
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 24 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 59000 X (nominal), 100000 X (calibrated)
    Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
    Cs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 2500 - 4500 nm
    Specimen HolderHolder: cartridge / Model: OTHER / Temperature: 82 K
    CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 4 / Applied symmetry: C1 (asymmetric) / Number of projections: 84000
    3D reconstructionAlgorithm: reference-based projection matching / Software: SPIDER / CTF correction: defocus group and wiener filter / Resolution: 13.2 A / Resolution method: FSC 0.5

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