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    - EMDB-1285: Structure of the ribosome-bound cricket paralysis virus IRES RNA. -

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    Basic information

    Entry
    Database: EMDB / ID: 1285
    TitleStructure of the ribosome-bound cricket paralysis virus IRES RNA.
    Sampleyeast 80S ribosome in complex with the CrPV IRES RNA
    SourceSaccharomyces cerevisiae / yeast / Baker's Yeast, Baker /
    Map dataComplex between the yeast 80S ribosome and the cricket paralysis virus IRES
    Methodsingle particle reconstruction, at 7.3 A resolution
    AuthorsSchuler M / Connell SR / Lescoute A / Giesebrecht J / Dabrowski M / Schroeer B / Mielke T / Penczek PA / Westhof E / Spahn CM
    CitationNat. Struct. Mol. Biol., 2006, 13, 1092-1096

    Nat. Struct. Mol. Biol., 2006, 13, 1092-1096 StrPapers
    Structure of the ribosome-bound cricket paralysis virus IRES RNA.
    Martin Schüler / Sean R Connell / Aurelie Lescoute / Jan Giesebrecht / Marylena Dabrowski / Birgit Schroeer / Thorsten Mielke / Pawel A Penczek / Eric Westhof / Christian M T Spahn

    DateDeposition: Oct 31, 2006 / Header (metadata) release: Oct 31, 2006 / Map release: Oct 31, 2007 / Last update: Oct 31, 2006

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1.2
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 1.2
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-2noq
    • Surface level: 1.2
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1285.map.gz (map file in CCP4 format, 105470 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    300 pix
    1.22 A/pix
    = 366. A
    300 pix
    1.22 A/pix
    = 366. A
    300 pix
    1.22 A/pix
    = 366. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.22 A
    Density
    Contour Level:2.76, 1.2 (movie #1):
    Minimum - Maximum-6.03604 - 12.0446
    Average (Standard dev.)0.0102696 (1.28183)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions300300300
    Origin-150-150-150
    Limit149149149
    Spacing300300300
    CellA=B=C: 366 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.221.221.22
    M x/y/z300300300
    origin x/y/z0.0000.0000.000
    length x/y/z366.000366.000366.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-184-184-183
    NX/NY/NZ368368368
    MAP C/R/S123
    start NC/NR/NS-150-150-150
    NC/NR/NS300300300
    D min/max/mean-6.03612.0450.010

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    Supplemental data

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    Sample components

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    Entire yeast 80S ribosome in complex with the CrPV IRES RNA

    EntireName: yeast 80S ribosome in complex with the CrPV IRES RNA / Number of components: 2

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

    Ribosome-eukaryoteName: yeast 80S ribosome / Eukaryote: ALL / Recombinant expression: No
    SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's Yeast /

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    Component #2: nucleic-acid, CrPV IRES

    Nucleic-acidName: CrPV IRES / Class: RNA / Structure: DOUBLE HELIX / Synthetic: No
    SourceSpecies: Saccharomyces cerevisiae / yeast / Baker /

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Details: Vitrification instrument: FEI Vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F30
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 39000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 500 - 3900 nm
    Specimen HolderHolder: Eucentric / Model: OTHER
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 341 / Scanner: PRIMESCAN / Sampling size: 4.7 microns

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 73313 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: projection matching / Software: SPIDER / CTF correction: Defocus groups / Resolution: 7.3 A / Resolution method: FSC 0.5

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