Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1325: Composition and three-dimensional EM structure of double affinity... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1325
    TitleComposition and three-dimensional EM structure of double affinity-purified, human prespliceosomal A complexes.
    SampleHuman prespliceosomal A Complex
    SourceHomo sapiens / human
    Map dataHuman spliceosomal A complex
    Methodsingle particle reconstruction, at 45 A resolution
    AuthorsBehzadnia N / Golas MM / Hartmuth K / Sander B / Kastner B / Deckert J / Dube P / Will CL / Urlaub H / Stark H / Luhrmann R
    CitationEMBO J., 2007, 26, 1737-1748

    EMBO J., 2007, 26, 1737-1748 StrPapers
    Composition and three-dimensional EM structure of double affinity-purified, human prespliceosomal A complexes.
    Nastaran Behzadnia / Monika M Golas / Klaus Hartmuth / Bjoern Sander / Berthold Kastner / Jochen Deckert / Prakash Dube / Cindy L Will / Henning Urlaub / Holger Stark / Reinhard Lührmann

    DateDeposition: Feb 16, 2007 / Header (metadata) release: Feb 16, 2007 / Map release: Feb 16, 2009 / Last update: Feb 16, 2007

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.065
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 0.065
    • 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_1325.map.gz (map file in CCP4 format, 3908 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    100 pix
    4.9 A/pix
    = 490. A
    100 pix
    4.9 A/pix
    = 490. A
    100 pix
    4.9 A/pix
    = 490. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 4.9 A
    Density
    Contour Level:0.06 (by emdb), 0.065 (movie #1):
    Minimum - Maximum-0.240983 - 0.564643
    Average (Standard dev.)0.00325364 (0.0341388)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions100100100
    Origin000
    Limit999999
    Spacing100100100
    CellA=B=C: 490 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z4.94.94.9
    M x/y/z100100100
    origin x/y/z0.0000.0000.000
    length x/y/z490.000490.000490.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-72-72-72
    NX/NY/NZ144144144
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS100100100
    D min/max/mean-0.2410.5650.003

    -
    Supplemental data

    -
    Sample components

    -
    Entire Human prespliceosomal A Complex

    EntireName: Human prespliceosomal A Complex / Number of components: 1

    -
    Component #1: cellular-component, Human prespliceosomal A Complex

    Cellular-componentName: Human prespliceosomal A Complex / a.k.a: Prespliceosome / Oligomeric Details: monomer / Recombinant expression: No
    SourceSpecies: Homo sapiens / human
    Source (natural)Organelle: nucleus / Cell: HeLa

    +
    Experimental details

    -
    Sample preparation

    Specimen stateparticle
    VitrificationCryogen name: ETHANE

    -
    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200FEG
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
    LensMagnification: 88000 X (nominal), 122000 X (calibrated) / Imaging mode: BRIGHT FIELD
    Specimen HolderModel: OTHER / Tilt Angle: 0 - 45 deg.
    CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

    -
    Image processing

    ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: RCT / Software: IMAGIC / Resolution: 45 A / Resolution method: FSC

    +
    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