Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1067: Domain movements of elongation factor eEF2 and the eukaryotic 80S... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1067
    TitleDomain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
    SampleRibosomal 80S-eEF2-sordarin complex from S. cerevisiae
    SourceSaccharomyces cerevisiae / yeast / Baker's yeast /
    Map datamap
    Methodsingle particle reconstruction, at 11.7 A resolution
    AuthorsSpahn CM / Frank J
    CitationEMBO J., 2004, 23, 1008-1019

    EMBO J., 2004, 23, 1008-1019 StrPapers
    Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
    Christian M T Spahn / Maria G Gomez-Lorenzo / Robert A Grassucci / Rene Jørgensen / Gregers R Andersen / Roland Beckmann / Pawel A Penczek / Juan P G Ballesta / Joachim Frank

    DateDeposition: Jan 5, 2004 / Header (metadata) release: Jan 6, 2004 / Map release: Jan 6, 2005 / Last update: Jan 5, 2004

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.0003
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by height
    • Surface level: 0.0003
    • Imaged by UCSF CHIMERA
    • Download
    3D viewer /

    View / / Stereo:
    Center
    Zoom
    Scale
    slabnear <=> far

    fix: /
    Orientation
    Orientation Rotation
    misc. /
    Show/hide
    Supplemental images

    Downloads & links

    -
    Map

    Fileemd_1067.map.gz (map file in CCP4 format, 7631 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    125 pix
    2.93 A/pix
    = 366.25 A
    125 pix
    2.93 A/pix
    = 366.25 A
    125 pix
    2.93 A/pix
    = 366.25 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.93 A
    Density
    Contour Level:0.000477, 0.0003 (movie #1):
    Minimum - Maximum-0.00084646 - 0.00169185
    Average (Standard dev.)1.69393e-05 (0.00020054)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions125125125
    Origin-62-62-62
    Limit626262
    Spacing125125125
    CellA=B=C: 366.25 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.932.932.93
    M x/y/z125125125
    origin x/y/z0.0000.0000.000
    length x/y/z366.250366.250366.250
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ0052
    NX/NY/NZ12812855
    MAP C/R/S123
    start NC/NR/NS-62-62-62
    NC/NR/NS125125125
    D min/max/mean-0.0010.0020.000

    -
    Supplemental data

    -
    Sample components

    -
    Entire Ribosomal 80S-eEF2-sordarin complex from S. cerevisiae

    EntireName: Ribosomal 80S-eEF2-sordarin complex from S. cerevisiae
    Number of components: 2
    MassTheoretical: 3.2 MDa

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

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

    -
    Component #2: protein, eEF2

    ProteinName: eEF2 / Recombinant expression: No
    SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast /

    +
    Experimental details

    -
    Sample preparation

    Specimen stateparticle
    VitrificationCryogen name: ETHANE

    -
    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 52000 X (calibrated) / Astigmatism: 100,000 X magnification / Cs: 2 mm / Imaging mode: BRIGHT FIELD
    Specimen HolderHolder: Oxford, cryo-transfer 3500 / Model: GATAN LIQUID NITROGEN / Temperature: 93 K
    CameraDetector: KODAK SO-163 FILM

    -
    Image acquisition

    Image acquisitionNumber of digital images: 86 / Scanner: ZEISS SCAI / Bit depth: 12

    -
    Image processing

    ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: back projection / Software: SPIDER / CTF correction: defocus group volumes / Resolution: 11.7 A / Resolution method: FSC 0.5

    -
    Atomic model buiding

    Output model

    +
    About Yorodumi

    -
    News

    -
    Sep 15, 2016. EM Navigator & Yorodumi renewed

    EM Navigator & Yorodumi renewed

    • New versions of EM Navigator and Yorodumi started

    Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

    -
    Aug 31, 2016. New EM Navigator & Yorodumi

    New EM Navigator & Yorodumi

    • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
    • Current version will continue as 'legacy version' for some time.

    Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

    +
    Apr 13, 2016. Omokage search got faster

    Omokage search got faster

    • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
    • Enjoy "shape similarity" of biomolecules, more!

    Related info.: Omokage search

    +
    Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

    Read more

    -
    Yorodumi

    Thousand views of thousand structures

    • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
    • All the functionalities will be ported from the levgacy version.
    • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

    Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

    Read more