Warning: Invalid argument supplied for foreach() in /var/www/html/emnavi/quick-emdb.php on line 1271

Warning: Invalid argument supplied for foreach() in /var/www/html/emnavi/quick-emdb.php on line 1271
EMDB-1976: Functional reconstitution of the 13-subunit human translation ini... - Yorodumi

Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1976: Functional reconstitution of the 13-subunit human translation ini... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1976
    TitleFunctional reconstitution of the 13-subunit human translation initiation factor eIF3.
    Keywordstranslation initiation / eukaryotic initiation factor 3 / ribosome / hepatitis C virus / internal ribosome entry site / proteasome / COP9 signalosome
    Sample12mer of the human eukaryotic translation initiation factor eIF3
    SourceHomo sapiens / human
    Map data3d reconstruction of 12mer human translation initiation factor eIF3
    Methodsingle particle reconstruction, at 29.3 A resolution
    AuthorsQuerol-Audi J / Sun C / Todorovic A / Bai Y / Villa N / Snyder M / Ashchyan J / Lewis C / Hartland A / Gradia S / Fraser CS / Doudna JA / Nogales E / Cate JHD
    CitationProc. Natl. Acad. Sci. U.S.A., 2011, 108, 20473-20478

    Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 20473-20478 StrPapers
    Functional reconstitution of human eukaryotic translation initiation factor 3 (eIF3).
    Chaomin Sun / Aleksandar Todorovic / Jordi Querol-Audí / Yun Bai / Nancy Villa / Monica Snyder / John Ashchyan / Christopher S Lewis / Abbey Hartland / Scott Gradia / Christopher S Fraser / Jennifer A Doudna / Eva Nogales / Jamie H D Cate

    DateDeposition: Oct 8, 2011 / Header (metadata) release: Nov 3, 2011 / Map release: Dec 21, 2011 / Last update: Oct 8, 2011

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 4.8
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 4.8
    • 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_1976.map.gz (map file in CCP4 format, 3457 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    96 pix
    4.36 A/pix
    = 418.56 A
    96 pix
    4.36 A/pix
    = 418.56 A
    96 pix
    4.36 A/pix
    = 418.56 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 4.36 A
    Density
    Contour Level:4.8 (by author), 4.8 (movie #1):
    Minimum - Maximum-5.17689 - 15.9619
    Average (Standard dev.)1.55009e-09 (0.999999)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions969696
    Origin000
    Limit959595
    Spacing969696
    CellA=B=C: 418.56 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z4.364.364.36
    M x/y/z969696
    origin x/y/z0.0000.0000.000
    length x/y/z418.560418.560418.560
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-56-56-55
    NX/NY/NZ112112112
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS969696
    D min/max/mean-5.17715.9620.000

    -
    Supplemental data

    -
    Sample components

    +
    Entire 12mer of the human eukaryotic translation initiation factor eIF3

    EntireName: 12mer of the human eukaryotic translation initiation factor eIF3
    Details: The sample was monodisperse / Number of components: 1
    Oligomeric State: Subcomplex containing 12 subunits, missing j subunit
    MassTheoretical: 700 kDa

    +
    Component #1: cellular-component, eIF3 a

    Cellular-componentName: eIF3 a / a.k.a: eIF3 a / Oligomeric Details: Monomer / Details: truncated version, contains residues 5-654 / Recombinant expression: Yes / Number of Copies: 1
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: Cytoplasm

    +
    Component #2: cellular-component, eIF3 b

    Cellular-componentName: eIF3 b / a.k.a: eIF3 b / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 700 kDa / Experimental: 700 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: Cytoplasm

    +
    Component #3: cellular-component, eIF3 c

    Cellular-componentName: eIF3 c / a.k.a: eIF3 c / Oligomeric Details: Monomer / Details: truncated version, contains residues 302-913 / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 700 kDa / Experimental: 700 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: Cytoplasm

    +
    Component #4: cellular-component, eIF3 d

    Cellular-componentName: eIF3 d / a.k.a: eIF3 d / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 700 kDa / Experimental: 700 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: Cytoplasm

    +
    Component #5: cellular-component, eIF3 e

    Cellular-componentName: eIF3 e / a.k.a: eIF3 e / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 700 kDa / Experimental: 700 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: Cytoplasm

    +
    Component #6: cellular-component, eIF3 f

    Cellular-componentName: eIF3 f / a.k.a: eIF3 f / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 700 kDa / Experimental: 700 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: Cytoplasm

    +
    Component #7: cellular-component, eIF3 g

    Cellular-componentName: eIF3 g / a.k.a: eIF3 g / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 700 kDa / Experimental: 700 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: Cytoplasm

    +
    Component #8: cellular-component, eIF3 h

    Cellular-componentName: eIF3 h / a.k.a: eIF3 h / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 700 kDa / Experimental: 700 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: Cytoplasm

    +
    Component #9: cellular-component, eIF3 i

    Cellular-componentName: eIF3 i / a.k.a: eIF3 i / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 700 kDa / Experimental: 700 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: Cytoplasm

    +
    Component #10: cellular-component, eIF3 k

    Cellular-componentName: eIF3 k / a.k.a: eIF3 k / Oligomeric Details: Monomer / Number of Copies: 1 / Recombinant expression: Yes
    MassTheoretical: 700 kDa / Experimental: 700 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: Cytoplasm

    +
    Component #11: cellular-component, eIF3 l

    Cellular-componentName: eIF3 l / a.k.a: eIF3 l / Oligomeric Details: Monomer / Number of Copies: 1 / Recombinant expression: Yes
    MassTheoretical: 700 kDa / Experimental: 700 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: Cytoplasm

    +
    Component #12: cellular-component, eIF3 m

    Cellular-componentName: eIF3 m / a.k.a: eIF3 m / Oligomeric Details: Monomer / Number of Copies: 1 / Recombinant expression: Yes
    MassTheoretical: 700 kDa / Experimental: 700 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: Cytoplasm

    +
    Experimental details

    -
    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.02 mg/ml
    Buffer solution: 20 mM HEPES, 120 mM KCl, 1 mM DTT, 1 mM EDTA, 1 mM EGTA, 3% trehalose
    pH: 7.5
    Support film200 mesh Cu grid
    StainingGrids with adsorbed protein stained with 3% w/v uranyl acetate for 40 seconds.
    VitrificationInstrument: NONE / Cryogen name: NONE

    -
    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 12
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 20 e/A2 / Illumination mode: SPOT SCAN
    LensMagnification: 49000 X (nominal)
    Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
    Cs: 6.3 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 1500 nm
    Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC
    CameraDetector: GENERIC TVIPS (4k x 4k)

    -
    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 400 / Number of projections: 12457
    Details: The particles were selected using an automatic selection program.
    Applied symmetry: C1 (asymmetric)
    3D reconstructionEuler angles: EMAN2 with initial and final angular steps of 25 and 10 degrees
    Software: EMAN2 / CTF correction: Whole image / Resolution: 29.3 A / Resolution method: FSC 0.5

    +
    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