Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - PDB-2wyy: CRYOEM MODEL OF THE VESICULAR STOMATITIS VIRUS -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: PDB / ID: 2wyy
    TitleCRYOEM MODEL OF THE VESICULAR STOMATITIS VIRUS
    DescriptorNUCLEOPROTEIN
    KeywordsVIRUS / RNA / NSRV / HELIX / VIRION / VIRAL NUCLEOPROTEIN
    Specimen sourceVESICULAR STOMATITIS INDIANA VIRUS / virus / VSV
    MethodElectron microscopy (10.6 A resolution / Helical / Vitreous ice (cryo EM))
    AuthorsGe, P. / Tsao, J. / Green, T.J. / Luo, M. / Zhou, Z.H.
    CitationScience, 2010, 327, 689-693

    Science, 2010, 327, 689-693 StrPapers
    Cryo-EM model of the bullet-shaped vesicular stomatitis virus.
    Peng Ge / Jun Tsao / Stan Schein / Todd J Green / Ming Luo / Z Hong Zhou

    DateDeposition: Nov 20, 2009 / Release: Feb 16, 2010 / Last modification: Aug 24, 2011

    -
    Structure visualization

    Movie
    • Biological unit as representative helical assembly
    • Imaged by Jmol
    • Download
    • Deposited structure unit
    • Imaged by Jmol
    • Download
    3D viewer /

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

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

    Downloads & links

    -
    Assembly

    Deposited unit
    A: NUCLEOPROTEIN
    C: NUCLEOPROTEIN
    D: NUCLEOPROTEIN
    F: NUCLEOPROTEIN
    H: NUCLEOPROTEIN
    I: NUCLEOPROTEIN
    J: NUCLEOPROTEIN
    K: NUCLEOPROTEIN
    L: NUCLEOPROTEIN
    M: NUCLEOPROTEIN
    R: POLY-URIDINE
    S: POLY-URIDINE

    502 kDa, 12 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    502,10912
    Polyers502,10912
    Non-polymers00
    Water0

    Omokage search
    #1
    A: NUCLEOPROTEIN
    C: NUCLEOPROTEIN
    D: NUCLEOPROTEIN
    F: NUCLEOPROTEIN
    H: NUCLEOPROTEIN
    I: NUCLEOPROTEIN
    J: NUCLEOPROTEIN
    K: NUCLEOPROTEIN
    L: NUCLEOPROTEIN
    M: NUCLEOPROTEIN
    R: POLY-URIDINE
    S: POLY-URIDINE
    x 15
    representative helical assembly / 7.53 MDa, 180 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    7,531,639180
    Polyers7,531,639180
    Non-polymers00
    Water0
    / Symmetry operations: (helical symmetry)x15
    Download / Omokage search
    #2idetical with deposited unit in distinct coordinate / helical asymmetric unit / Symmetry operations: (helical symmetry)x1
    HAUidetical with deposited unit in distinct coordinate / helical asymmetric unit, std helical frame / Symmetry operations: (transform to helical frame)x1

    -
    Components

    #1polypeptide(L) / NUCLEOPROTEIN / NUCLEOCAPSID PROTEIN, NP, PROTEIN N / Source: VESICULAR STOMATITIS INDIANA VIRUS (gene. exp.) / References: UniProt: P03521
    #2RNA chain / POLY-URIDINE

    +
    Experimental details

    -
    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: HELICAL / Specimen type: VITREOUS ICE (CRYO EM)

    -
    Sample preparation

    Assembly of specimen
    NameAggregation stateDetailsID
    VSV (INDIANA)FILAMENT1
    DATA AQUISITION2
    Buffer solutionName: 100MM NACL, 10NM TRIS, 1MM EDTA
    Sample preparationpH: 7.4
    VitrificationDetails: CRYOGEN - ETHANE, HUMIDITY - 50, TEMPERATURE - 80, INSTRUMENT - MANUAL PLUNGER, METHOD- MANUAL BLOT 1 SECOND BEFORE PLUNGING, DETAILS - VITRIFICATION CARRIED OUT IN OPEN ROOM.

    -
    Electron microscopy imaging

    MicroscopyDate: Jan 5, 2007
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: SPOT SCAN
    Electron lensNominal magnification: 59000 X / Calibrated magnification: 98000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2 mm
    Specimen holderTemperature: 80 K
    CameraType: TIETZ CCD
    EM image scansNumber digital images: 212
    Radiation wavelengthRelative weight: 1

    -
    Processing

    Image selectionSoftware name: EMAN
    3D reconstructionMethod: PROJECTION MATCHING / Resolution: 10.6 A
    Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1663.
    Atomic model buildingMethod: RIGID BODY / Ref protocol: RIGID BODY REFINEMENT / Ref space: REAL / Target criteria: CROSS-CORRELATION
    Least-squares processHighest resolution: 1 A
    Refine hist #LASTHighest resolution: 1 A
    Number of atoms included #LASTProtein: 32820 / Nucleic acid: 1800 / Ligand: 0 / Solvent: 0 / Total: 34620

    +
    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