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    - EMDB-5329: Cryo EM reconstruction of mammalian 80S ribosome in rotated PRE s... -

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    Basic information

    Entry
    Database: EMDB / ID: 5329
    TitleCryo EM reconstruction of mammalian 80S ribosome in rotated PRE state 2
    Keywords80S ribosome / mammalian / elongation cycle / tRNA
    Sample80S-PRE-rotated-2 complex from rabbit (Oryctolagus cuniculus) liver
    SourceOryctolagus cuniculus / mammal / rabbit /
    Map data80S mammalian ribosome
    Methodsingle particle reconstruction, at 10.6 A resolution
    AuthorsBudkevich T / Giesebrecht J / Altman R / Munro J / Mielke T / Nierhaus K / Blanchard S / Spahn C
    CitationMol. Cell, 2011, 44, 214-224

    Mol. Cell, 2011, 44, 214-224 StrPapers
    Structure and dynamics of the mammalian ribosomal pretranslocation complex.
    Tatyana Budkevich / Jan Giesebrecht / Roger B Altman / James B Munro / Thorsten Mielke / Knud H Nierhaus / Scott C Blanchard / Christian M T Spahn

    DateDeposition: Jul 12, 2011 / Header (metadata) release: Jul 28, 2011 / Map release: Nov 9, 2011 / Last update: Jul 12, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1000
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 1000
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-3j0q
    • Surface level: 1000
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5329.map.gz (map file in CCP4 format, 22783 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    180 pix
    2.52 A/pix
    = 453.6 A
    180 pix
    2.52 A/pix
    = 453.6 A
    180 pix
    2.52 A/pix
    = 453.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.52 A
    Density
    Contour Level:1000 (by author), 1000 (movie #1):
    Minimum - Maximum-2542.37280273 - 17103.23632813
    Average (Standard dev.)275.67153931 (1215.57641602)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions180180180
    Origin-90-90-89
    Limit898990
    Spacing180180180
    CellA=B=C: 453.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.522.522.52
    M x/y/z180180180
    origin x/y/z0.0000.0000.000
    length x/y/z453.600453.600453.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-90-90-89
    NC/NR/NS180180180
    D min/max/mean-2542.37317103.236275.672

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    Supplemental data

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    Sample components

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    Entire 80S-PRE-rotated-2 complex from rabbit (Oryctolagus cuniculus) liver

    EntireName: 80S-PRE-rotated-2 complex from rabbit (Oryctolagus cuniculus) liver
    Details: Sample was re-associated from subunits / Number of components: 5 / Oligomeric State: monomer
    MassExperimental: 4 MDa / Measured by: Sedimentation

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    Component #1: ribosome-eukaryote, 80S ribosome

    Ribosome-eukaryoteName: 80S ribosome / Eukaryote: LSU 60S, SSU 40S / Recombinant expression: No
    MassTheoretical: 4 MDa
    SourceSpecies: Oryctolagus cuniculus / mammal / rabbit /
    Source (natural)Organ or tissue: liver

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionpH: 7.5
    Support filmQuantifoil grids
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 77 K / Humidity: 100 %
    Method: Flash-frozen in liquid ethane on carbon coated Quantifoil grids
    Details: Vitrification instrument: VitroBot (FEI)

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    Electron microscopy imaging

    ImagingMicroscope: FEI POLARA 300 / Date: Oct 17, 2006
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: SPOT SCAN
    LensMagnification: 39000 X (nominal), 65520 X (calibrated)
    Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 4000 nm
    Specimen HolderHolder: Cartridge / Model: GATAN HELIUM / Temperature: 77 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 87 / Scanner: PRIMESCAN / Sampling size: 4.7 microns

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    Image processing

    ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 23347
    3D reconstructionAlgorithm: Multi-particle refinement / Software: SPIDER / CTF correction: By defocus groups
    Details: Several rounds of multireference 3D projection refinement
    Resolution: 10.6 A / Resolution method: FSC 0.5

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    Output model

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