Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1675: Keap1 homodimer -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1675
    TitleKeap1 homodimer
    KeywordsNrf2 / oxidative stress / single particle analysis / transmission electron microscopy / three-dimensional reconstruction
    SampleKeap1
    SourceMus musculus / mammal / Mouse /
    Map dataThis is an image of a surface rendered side-view of Keap1
    Methodsingle particle reconstruction, at 24 A resolution
    AuthorsOgura T / Tong KI / Mio K / Maruyama Y / Kurokawa H / Sato C / Yamamoto M
    CitationProc. Natl. Acad. Sci. U.S.A., 2010, 107, 2842-2847

    Proc. Natl. Acad. Sci. U.S.A., 2010, 107, 2842-2847 StrPapers
    Keap1 is a forked-stem dimer structure with two large spheres enclosing the intervening, double glycine repeat, and C-terminal domains.
    Toshihiko Ogura / Kit I Tong / Kazuhiro Mio / Yuusuke Maruyama / Hirofumi Kurokawa / Chikara Sato / Masayuki Yamamoto

    DateDeposition: Jan 8, 2010 / Header (metadata) release: Apr 26, 2011 / Map release: Apr 26, 2011 / Last update: Jan 8, 2010

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 215
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by cylindrical radius
    • Surface level: 215
    • 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_1675.map.gz (map file in CCP4 format, 3908 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    100 pix
    1.92 A/pix
    = 192. A
    100 pix
    1.92 A/pix
    = 192. A
    100 pix
    1.92 A/pix
    = 192. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.92 A
    Density
    Contour Level:215 (by emdb), 215 (movie #1):
    Minimum - Maximum0 - 255
    Average (Standard dev.)114.131 (32.4104)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions100100100
    Origin000
    Limit999999
    Spacing100100100
    CellA=B=C: 192 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.921.921.92
    M x/y/z100100100
    origin x/y/z0.0000.0000.000
    length x/y/z192.000192.000192.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ000
    NX/NY/NZ121121121
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS100100100
    D min/max/mean0.000255.000114.131

    -
    Supplemental data

    -
    Sample components

    -
    Entire Keap1

    EntireName: Keap1 / Details: The sample was monodisperse / Number of components: 1 / Oligomeric State: One homodimer of Keap1
    MassTheoretical: 141 kDa / Experimental: 155 kDa

    -
    Component #1: protein, Keap1

    ProteinName: Keap1 / a.k.a: Keap1 / Oligomeric Details: Dimer / Recombinant expression: Yes / Number of Copies: 2
    MassTheoretical: 141 kDa / Experimental: 155 kDa
    SourceSpecies: Mus musculus / mammal / Mouse /
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: Cytoplasm

    +
    Experimental details

    -
    Sample preparation

    Specimen stateparticle
    VitrificationInstrument: NONE / Cryogen name: NONE

    -
    Electron microscopy imaging

    ImagingMicroscope: JEOL 100CX
    Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: OTHER
    LensImaging mode: BRIGHT FIELD
    Specimen HolderHolder: Top entry / Model: JEOL

    -
    Image acquisition

    Image acquisitionNumber of digital images: 92 / Sampling size: 10 microns / Bit depth: 16

    -
    Image processing

    ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic)
    3D reconstructionAlgorithm: Echo-correlation method / Software: SPINNS / CTF correction: Each particle / Resolution: 24 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