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    Yorodumi
    - EMDB-1122: Visualizing tmRNA entry into a stalled ribosome. -

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    Basic information

    Entry
    Database: EMDB / ID: 1122
    TitleVisualizing tmRNA entry into a stalled ribosome.
    Sample70S-Psite tRNA - mRNA - EF-Tu.GDP - alanylated tmRNA - SmpB - Kirromycin - S1
    SourceThermus thermophilus hb8 / bacteria / thermophilic
    Map datathis is a ribosome consisting 70S + Psite tRNA + mRNA + EF-Tu.GDP + alanylated tmRNA + SmpB + Kirromycin + S1
    Methodsingle particle reconstruction, at 13 A resolution
    AuthorsValle M / Gillet R / Kaur S / Henne A / Ramakrishnan V / Frank J
    CitationScience, 2003, 300, 127-130

    Science, 2003, 300, 127-130 StrPapers
    Visualizing tmRNA entry into a stalled ribosome.
    Mikel Valle / Reynald Gillet / Sukhjit Kaur / Anke Henne / V Ramakrishnan / Joachim Frank

    DateDeposition: Mar 24, 2005 / Header (metadata) release: Apr 11, 2005 / Map release: Apr 11, 2005 / Last update: Mar 24, 2005

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 42
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by height
    • Surface level: 42
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view with fitted model
    • Atomic models: : PDB-1zc8
    • Surface level: 42
    • Imaged by UCSF CHIMERA
    • Download
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1122.map.gz (map file in CCP4 format, 10720 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    140 pix
    2.82 A/pix
    = 394.8 A
    140 pix
    2.82 A/pix
    = 394.8 A
    140 pix
    2.82 A/pix
    = 394.8 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:54.9, 42 (movie #1):
    Minimum - Maximum-147.485 - 313.886
    Average (Standard dev.)2.87458 (28.7702)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions140140140
    Origin-70-70-70
    Limit696969
    Spacing140140140
    CellA=B=C: 394.8 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.822.822.82
    M x/y/z140140140
    origin x/y/z0.0000.0000.000
    length x/y/z394.800394.800394.800
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-220-220-220
    NX/NY/NZ441441441
    MAP C/R/S123
    start NC/NR/NS-70-70-70
    NC/NR/NS140140140
    D min/max/mean-147.485313.8862.875

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    Supplemental data

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    Sample components

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    Entire 70S-Psite tRNA - mRNA - EF-Tu.GDP - alanylated tmRNA - SmpB - Kir...

    EntireName: 70S-Psite tRNA - mRNA - EF-Tu.GDP - alanylated tmRNA - SmpB - Kirromycin - S1
    Number of components: 5

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    Component #1: ribosome-prokaryote, 70S Ribosome

    Ribosome-prokaryoteName: 70S Ribosome / Details: Thermus thermophilus / Prokaryote: ALL / Recombinant expression: No
    SourceSpecies: Thermus thermophilus hb8 / bacteria / thermophilic

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    Component #2: nucleic-acid, tRNA

    Nucleic-acidName: tRNA / Class: T-RNA / Details: P site / Structure: SINGLE STRANDED / Synthetic: No
    SourceSpecies: Thermus thermophilus hb8 / bacteria / thermophilic

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    Component #3: protein, EF-Tu

    ProteinName: EF-Tu / Recombinant expression: No
    SourceSpecies: Thermus thermophilus hb8 / bacteria / thermophilic

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    Component #4: ligand, tmRNA

    LigandName: tmRNA / Recombinant expression: No
    SourceSpecies: Thermus thermophilus hb8 / bacteria / thermophilic

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    Component #5: protein, SmpB

    ProteinName: SmpB / Recombinant expression: No
    SourceSpecies: Thermus thermophilus hb8 / bacteria / thermophilic

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 25 mM Hepes-KOH pH 7.5, 30 mM NH4Cl, 7mM MgCl2, 2 mM ATP, 6 mM PEP, 10g/ml PK
    pH: 7.5
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 93 K / Humidity: 90 % / Method: Blot for 2 seconds before plunging
    Details: Vitrification instrument: two side blotting plunger

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20 / Date: Aug 1, 2002
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 49000 X (nominal), 52000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1450 - 3700 nm
    Specimen HolderHolder: Cryo transfer / Model: GATAN LIQUID NITROGEN / Temperature: 93 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 44 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 12 / OD range: 1.2

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 27644 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: reference projection / Software: SPIDER / CTF correction: defocus groups / Resolution: 13 A / Resolution method: FSC at 0.15 cut-off / Euler angles: SPIDER definition

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    Atomic model buiding

    Modeling #1Software: manual / Refinement protocol: rigid body / Target criteria: cross correlation coefficient
    Details: Protocol: Rigid Body. The domains were separately fitted by manual docking using program O
    Output model

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