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    - EMDB-5224: Human 80S ribosome in situ, untreated -

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    Basic information

    Entry
    Database: EMDB / ID: 5224
    TitleHuman 80S ribosome in situ, untreated
    Keywordshuman 80S ribosome / puromycin / in situ / cytosol / polysome / polyribosome / protein synthesis / translation / 3D cryoEM / tomography / cellular tomography
    SampleHuman 80S ribosome in situ, untreated
    SourceHomo sapiens / human
    Map dataThis is a map of a tomographic average of a human 80S ribosome in situ
    Methodsubtomogram averaging, at 39 A resolution
    AuthorsBrandt F / Carlson L-A / Hartl FU / Baumeister W / Grunewald K
    CitationMol. Cell, 2010, 39, 560-569

    Mol. Cell, 2010, 39, 560-569 StrPapers
    The three-dimensional organization of polyribosomes in intact human cells.
    Florian Brandt / Lars-Anders Carlson / F Ulrich Hartl / Wolfgang Baumeister / Kay Grünewald

    DateDeposition: Aug 10, 2010 / Header (metadata) release: Dec 9, 2010 / Map release: Dec 9, 2010 / Last update: Aug 10, 2010

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.9
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 0.9
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_5224.map.gz (map file in CCP4 format, 433 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    48 pix
    8.21 A/pix
    = 394.08 A
    48 pix
    8.21 A/pix
    = 394.08 A
    48 pix
    8.21 A/pix
    = 394.08 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 8.21 A
    Density
    Contour Level:0.9 (by author), 0.9 (movie #1):
    Minimum - Maximum-2.09170914 - 4.06884241
    Average (Standard dev.)0E-8 (0.99999547)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions484848
    Origin000
    Limit474747
    Spacing484848
    CellA=B=C: 394.08002 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z8.218.218.21
    M x/y/z484848
    origin x/y/z0.0000.0000.000
    length x/y/z394.080394.080394.080
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-99-99-99
    NX/NY/NZ200200200
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS484848
    D min/max/mean-2.0924.069-0.000

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    Supplemental data

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    Sample components

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    Entire Human 80S ribosome in situ, untreated

    EntireName: Human 80S ribosome in situ, untreated / Details: Cytosolic ribosomes in situ / Number of components: 1
    Oligomeric State: One 80S ribosome within mixed cellular polysomes
    MassMeasured by: Sedimentation, 80S

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    Component #1: ribosome-eukaryote, cytosolic 80S ribosome

    Ribosome-eukaryoteName: cytosolic 80S ribosome / Eukaryote: ALL / Recombinant expression: No
    SourceSpecies: Homo sapiens / human

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: Cellular medium, DMEM (Gibco) supplemented with 10% foetal calf serum, 37C and 5% CO2
    pH: 7.5
    Support filmC-flat 2/1, holey carbon gold grid
    StainingCells grown on grids, vitrification
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 77 K / Method: Blot for 2 s before plunging
    Details: Vitrification instrument: plunger. Vitrification carried out in air

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM300FEG/T / Date: Jul 7, 2008
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 80 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 17500 X (nominal), 17500 X (calibrated)
    Astigmatism: objective lens astigmatism was corrected at 50,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 5000 - 7000 nm / Energy filter: GIF2002 / Energy window: 0-20 eV
    Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder.
    Model: GATAN LIQUID NITROGEN / Tilt Angle: -65 - 65 deg. / Temperature: 77 K ( 77 - K)
    CameraDetector: GATAN MULTISCAN

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    Image processing

    ProcessingMethod: subtomogram averaging / Number of subtomograms: 1911 / Applied symmetry: C1 (asymmetric) / Number of class averages: 1
    Details: Individual particle subvolumes were automatically selected by CCC threshold.
    3D reconstructionAlgorithm: weighted back-projection / Software: EM / Details: exact weighting / Resolution: 39 A / Resolution method: FSC 0.5

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