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    Yorodumi
    - EMDB-5386: tmRNA translocation and MLD-loading on the ribosome: a 70S-tmRNA-... -

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    Basic information

    Entry
    Database: EMDB / ID: 5386
    TitletmRNA translocation and MLD-loading on the ribosome: a 70S-tmRNA-EF-G complex
    Keywordstrans-translation / MLD-loading / translocation / tmRNA / EF-G / SmpB
    SampleComplex of 70S-tmRNA-SmpB-EF-G
    SourceEscherichia coli / bacteria /
    Map dataOverall view of the 70S-tmRNA-SmpB-EF-G complex
    Methodsingle particle reconstruction, at 8.3 A resolution
    AuthorsRamrath DJF / Yamamoto H / Rother K / Wittek D / Pech M / Mielke T / Loerke J / Scheerer P / Ivanov P / Teraoka Y / Shpanchenko O / Nierhaus KH / Spahn CMT
    CitationNature, 2012, 485, 526-529

    Nature, 2012, 485, 526-529 StrPapers
    The complex of tmRNA-SmpB and EF-G on translocating ribosomes.
    David J F Ramrath / Hiroshi Yamamoto / Kristian Rother / Daniela Wittek / Markus Pech / Thorsten Mielke / Justus Loerke / Patrick Scheerer / Pavel Ivanov / Yoshika Teraoka / Olga Shpanchenko / Knud H Nierhaus / Christian M T Spahn

    DateDeposition: Jan 20, 2012 / Header (metadata) release: Feb 21, 2012 / Map release: Apr 30, 2012 / Last update: Jan 20, 2012

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 2
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 2
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-4v6t
    • Surface level: 2
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5386.map.gz (map file in CCP4 format, 105470 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    300 pix
    1.26 A/pix
    = 378. A
    300 pix
    1.26 A/pix
    = 378. A
    300 pix
    1.26 A/pix
    = 378. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.26 A
    Density
    Contour Level:2 (by author), 2 (movie #1):
    Minimum - Maximum-3.38914657 - 9.00063801
    Average (Standard dev.)0.20524462 (0.75120121)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions300300300
    Origin-150-150-150
    Limit149149149
    Spacing300300300
    CellA=B=C: 378 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.261.261.26
    M x/y/z300300300
    origin x/y/z0.0000.0000.000
    length x/y/z378.000378.000378.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-150-150-150
    NC/NR/NS300300300
    D min/max/mean-3.3899.0010.205

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    Supplemental data

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    Sample components

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    Entire Complex of 70S-tmRNA-SmpB-EF-G

    EntireName: Complex of 70S-tmRNA-SmpB-EF-G / Details: the sample was flash frozen in liquid ethane / Number of components: 5 / Oligomeric State: Monomer
    MassTheoretical: 3 MDa / Experimental: 3 MDa / Measured by: Sedimentation

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    Component #1: ribosome-prokaryote, Ribosome

    Ribosome-prokaryoteName: Ribosome / a.k.a: 70S-tmRNA-EFG / Details: the complex was stalled with fusidic acid / Prokaryote: ALL / Recombinant expression: No
    MassTheoretical: 3.05 MDa / Experimental: 3 MDa
    SourceSpecies: Escherichia coli / bacteria / / Strain: CAN20

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.15 mg/ml
    Buffer solution: 20 mM HEPES-KOH, pH 7.6, 4.5 mM Mg(Ac)2, 150 mM NH4Ac, 4 mM b-mercaptoethanol, 2 mM spermidine, and 0.05 mM spermine
    pH: 7.6
    Support filmQuantifoil R3-3 Cu 300 mesh with 2 nm carbon support film
    Stainingflash frozen in liquid ethane
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 96.15 K / Humidity: 100 % / Method: blot for 10 seconds before plunging / Details: Vitrification instrument: FEI VITROBOT

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    Electron microscopy imaging

    ImagingMicroscope: FEI POLARA 300 / Date: Dec 8, 2009
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: SPOT SCAN
    LensMagnification: 39000 X (nominal), 39000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 5000 nm
    Specimen HolderHolder: Cartridge / Model: GATAN HELIUM / Temperature: 77.15 K ( 77.15 - 81.15 K)
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 302 / Scanner: PRIMESCAN / Sampling size: 4.7 microns / Bit depth: 16

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 68842 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: angular refinement / Software: Spider / CTF correction: Defocus groups / Resolution: 8.3 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: Chimera / Refinement protocol: rigid body / Target criteria: cross-correlation / Refinement space: REAL / Details: Protocol: Rigid Body
    Input PDB model: 3R8S
    Output model

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