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    Yorodumi
    - EMDB-1093: Cryo-EM visualization of a viral internal ribosome entry site bou... -

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    Basic information

    Entry
    Database: EMDB / ID: 1093
    TitleCryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor.
    SampleHuman ribosome 80s
    SourceHomo sapiens / human
    Map datamap
    Methodsingle particle reconstruction, at 18.3 A resolution
    AuthorsSpahn CM / Frank J
    CitationCell, 2004, 118, 465-475

    Cell, 2004, 118, 465-475 StrPapers
    Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor.
    Christian M T Spahn / Eric Jan / Anke Mulder / Robert A Grassucci / Peter Sarnow / Joachim Frank

    DateDeposition: Aug 10, 2004 / Header (metadata) release: Aug 10, 2004 / Map release: Nov 10, 2004 / Last update: Aug 10, 2004

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.00047
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by height
    • Surface level: 0.00047
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1093.map.gz (map file in CCP4 format, 7631 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    125 pix
    3.66 A/pix
    = 457.5 A
    125 pix
    3.66 A/pix
    = 457.5 A
    125 pix
    3.66 A/pix
    = 457.5 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 3.66 A
    Density
    Contour Level:0.000488, 0.00047 (movie #1):
    Minimum - Maximum-0.00123335 - 0.00223165
    Average (Standard dev.)2.75366e-05 (0.000244317)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions125125125
    Origin-62-62-62
    Limit626262
    Spacing125125125
    CellA=B=C: 457.5 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z3.663.663.66
    M x/y/z125125125
    origin x/y/z0.0000.0000.000
    length x/y/z457.500457.500457.500
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-96-56-288
    NX/NY/NZ192112576
    MAP C/R/S123
    start NC/NR/NS-62-62-62
    NC/NR/NS125125125
    D min/max/mean-0.0010.0020.000

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    Supplemental data

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    Sample components

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    Entire Human ribosome 80s

    EntireName: Human ribosome 80s / Number of components: 1

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    Component #1: ribosome-eukaryote, Human ribosome 80s

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

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    VitrificationCryogen name: ETHANE

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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), 38000 X (calibrated)
    Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
    Cs: 2.26 mm / Imaging mode: BRIGHT FIELD
    Specimen HolderHolder: FEI Polara cartridge system / Model: OTHER / Temperature: 84 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionScanner: ZEISS SCAI / Sampling size: 14 microns

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    Image processing

    ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Back projection / Software: SPIDER / CTF correction: defocus group volumes / Resolution: 18.3 A / Resolution method: FSC 0.5

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