Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1864: Cryo-EM reconstruction of native and expanded Turnip Crinkle virus -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1864
    TitleCryo-EM reconstruction of native and expanded Turnip Crinkle virus
    KeywordsTurnip crinkle virus / genomic RNA structure / genome uncoating / ssRNA virus
    SampleTurnip crinkle virus
    SourceTurnip crinkle virus / virus
    Map data3D cryo-EM reconstruction of the expanded form of Turnip Crinkle Virus
    Methodsingle particle (icosahedral) reconstruction, at 17 A resolution
    AuthorsBakker SE / Robottom J / Pearson AR / Stockley PG / Ranson NA
    CitationJ. Mol. Biol., 2012, 417, 65-78

    primary. J. Mol. Biol., 2012, 417, 65-78 StrPapers
    Isolation of an asymmetric RNA uncoating intermediate for a single-stranded RNA plant virus.
    Saskia E Bakker / Robert J Ford / Amy M Barker / Janice Robottom / Keith Saunders / Arwen R Pearson / Neil A Ranson / Peter G Stockley

    1. J. Mol. Biol., 1986, 191, 625-638 StrPapers
    Structure and assembly of turnip crinkle virus. I. X-ray crystallographic structure analysis at 3.2 A resolution.
    J M Hogle / A Maeda / S C Harrison

    DateDeposition: Jan 25, 2011 / Header (metadata) release: Jul 9, 2012 / Map release: Jul 9, 2012 / Last update: Jan 25, 2011

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 3.2
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 3.2
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view with fitted model
    • Atomic models: : PDB-3zx9
    • Surface level: 3.2
    • 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_1864.map.gz (map file in CCP4 format, 54001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    240 pix
    1.89 A/pix
    = 453.6 A
    240 pix
    1.89 A/pix
    = 453.6 A
    240 pix
    1.89 A/pix
    = 453.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.89 A
    Density
    Contour Level:3.2 (by author), 3.2 (movie #1):
    Minimum - Maximum-1.86774302 - 4.17278814
    Average (Standard dev.)0.16210388 (1.48636842)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions240240240
    Origin-120-120-120
    Limit119119119
    Spacing240240240
    CellA=B=C: 453.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.891.891.89
    M x/y/z240240240
    origin x/y/z0.0000.0000.000
    length x/y/z453.600453.600453.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-160-160-159
    NX/NY/NZ320320320
    MAP C/R/S123
    start NC/NR/NS-120-120-120
    NC/NR/NS240240240
    D min/max/mean-1.8684.1730.162

    -
    Supplemental data

    -
    Sample components

    -
    Entire Turnip crinkle virus

    EntireName: Turnip crinkle virus / Number of components: 1 / Oligomeric State: Icosahedral virus
    MassTheoretical: 6.8 MDa

    -
    Component #1: virus, Turnip crinkle virus

    VirusName: Turnip crinkle virus / a.k.a: Turnip crinkle virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
    MassTheoretical: 6.8 MDa
    SpeciesSpecies: Turnip crinkle virus / virus
    Source (natural)Host Species: Brassica rapa subsp. rapa / plant / image: Brassica rapa
    Shell #1Name of element: Expanded / Diameter: 380 A / T number(triangulation number): 3

    +
    Experimental details

    -
    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 3 mg/ml / Buffer solution: 100 mM Tris pH 8.5, 5 mM EDTA / pH: 8.5
    Support film400 mesh copper grid
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 77 K / Method: Blot 1.6 seconds before plunging
    Details: Vitrification instrument: Double sided automated blotter and plunger

    -
    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), 52911 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm
    Specimen HolderHolder: Gatan 626 / Model: GATAN LIQUID NITROGEN
    CameraDetector: KODAK SO-163 FILM

    -
    Image acquisition

    Image acquisitionNumber of digital images: 41 / Scanner: OTHER / Sampling size: 10 microns

    -
    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 5121 / Number of class averages: 110 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: Icosahedral / Software: SPIDER / CTF correction: Phase-flipping each particle / Resolution: 17 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