Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1996: Bubblegrams reveal the inner body of bacteriophage phiKZ -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1996
    TitleBubblegrams reveal the inner body of bacteriophage phiKZ
    Keywordsinner body / core protein / asymmetric reconstruction / phiKZ / protein mapping
    SamplephiKZ mature phage
    SourcePseudomonas phage phiKZ / virus / phiKZ
    Map dataThis is the inner body structure of bacteriophage phiKZ.
    Methodsingle particle reconstruction, at 37 A resolution
    AuthorsWu W / Thomas JA / Cheng N / Black LW / Steven AC
    CitationScience, 2012, 335, 182-182

    Science, 2012, 335, 182-182 StrPapers
    Bubblegrams reveal the inner body of bacteriophage φKZ.
    Weimin Wu / Julie A Thomas / Naiqian Cheng / Lindsay W Black / Alasdair C Steven

    DateDeposition: Nov 23, 2011 / Header (metadata) release: Jan 13, 2012 / Map release: Jan 13, 2012 / Last update: Nov 23, 2011

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 750
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 750
    • 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_1996.map.gz (map file in CCP4 format, 16001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    160 pix
    10.03 A/pix
    = 1604.16 A
    160 pix
    10.03 A/pix
    = 1604.16 A
    160 pix
    10.03 A/pix
    = 1604.16 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 10.026 A
    Density
    Contour Level:750 (by author), 750 (movie #1):
    Minimum - Maximum-5409.6 - 9004.46
    Average (Standard dev.)10.7033 (238.579)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions160160160
    Origin-80-80-80
    Limit797979
    Spacing160160160
    CellA=B=C: 1604.16 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z10.02610.02610.026
    M x/y/z160160160
    origin x/y/z0.0000.0000.000
    length x/y/z1604.1601604.1601604.160
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-56-56-55
    NX/NY/NZ112112112
    MAP C/R/S123
    start NC/NR/NS-80-80-80
    NC/NR/NS160160160
    D min/max/mean-5409.5959004.45910.703

    -
    Supplemental data

    -
    Sample components

    -
    Entire phiKZ mature phage

    EntireName: phiKZ mature phage / Number of components: 5
    Oligomeric State: Inner body inside the capsid surrounding by DNA

    -
    Component #1: virus, Pseudomonas phage phiKZ

    VirusName: Pseudomonas phage phiKZ / a.k.a: phiKZ / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
    SpeciesSpecies: Pseudomonas phage phiKZ / virus / phiKZ
    Source (natural)Host Species: Pseudomonas aeruginosa / bacteria / Host category: BACTERIA(EUBACTERIA)

    +
    Experimental details

    -
    Sample preparation

    Specimen stateparticle
    VitrificationInstrument: NONE / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 40 %

    -
    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200FEG / Date: Jan 20, 2011
    Details: Image pairs. First low dose image, 12 electrons per angstrom squared, then high dose to get radiation damage (same dose but longer time), dose about 5-fold of low dose.
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 12 e/A2 / Illumination mode: SPOT SCAN
    LensMagnification: 38000 X (nominal), 38000 X (calibrated) / Astigmatism: condenser and objective lens astigmatism / Cs: 2 mm / Imaging mode: OTHER / Defocus: 800 - 1500 nm
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 100 K
    CameraDetector: KODAK SO-163 FILM

    -
    Image acquisition

    Image acquisitionNumber of digital images: 95 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 16

    -
    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 2775 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Projection match / Software: EMAN / CTF correction: Micrograph
    Details: Projection match method was used to determine the unique vertex and the orientation of tail. The inner body was solved directly from 2D data without using any initial model.
    Resolution: 37 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