Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1246: Distribution and three-dimensional structure of AIDS virus envelo... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1246
    TitleDistribution and three-dimensional structure of AIDS virus envelope spikes.
    SampleEnvelope Spike on the surface of SIVmac239 virus with truncated cytoplasmic tail
    SourceSimian immunodeficiency virus / virus
    Map data3D map of SIVmac239 envelope spike. It is the 3D averaged volume of all spikes including both "top/bottom view" and "side view" subsets (supplementary method of the reference). Author's threshold 2.65. It should be loaded together with the associated viral membrane map (SIVmac239_Vir_memb.map, EMD-1247, author's threshold 2.25 ).
    Methodsubtomogram averaging, at 32 A resolution
    AuthorsZhu P / Liu J / Bess J / Chertova E / Lifson JD / Grise H / Ofek GA / Taylor KA / Roux KH
    CitationNature, 2006, 441, 847-852

    Nature, 2006, 441, 847-852 StrPapers
    Distribution and three-dimensional structure of AIDS virus envelope spikes.
    Ping Zhu / Jun Liu / Julian Bess / Elena Chertova / Jeffrey D Lifson / Henry Grisé / Gilad A Ofek / Kenneth A Taylor / Kenneth H Roux

    DateDeposition: Jul 21, 2006 / Header (metadata) release: Jul 25, 2006 / Map release: Jul 25, 2006 / Last update: Jul 21, 2006

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 2.65
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by cylindrical radius
    • Surface level: 2.65
    • 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_1246.map.gz (map file in CCP4 format, 1459 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    72 pix
    5.56 A/pix
    = 400.32 A
    72 pix
    5.56 A/pix
    = 400.32 A
    72 pix
    5.56 A/pix
    = 400.32 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 5.56 A
    Density
    Contour Level:1.34, 2.65 (movie #1):
    Minimum - Maximum-7.62291 - 12.3396
    Average (Standard dev.)-2.84499e-08 (0.901928)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions727272
    Origin-36-36-36
    Limit353535
    Spacing727272
    CellA=B=C: 400.32 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z5.565.565.56
    M x/y/z727272
    origin x/y/z0.0000.0000.000
    length x/y/z400.320400.320400.320
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-64-64-64
    NX/NY/NZ128128128
    MAP C/R/S123
    start NC/NR/NS-36-36-36
    NC/NR/NS727272
    D min/max/mean-7.62312.340-0.000

    -
    Supplemental data

    -
    Sample components

    -
    Entire Envelope Spike on the surface of SIVmac239 virus with truncated c...

    EntireName: Envelope Spike on the surface of SIVmac239 virus with truncated cytoplasmic tail
    Details: The virus was AT-2 treated to eliminate the infectivity.
    Number of components: 1 / Oligomeric State: Trimer
    MassTheoretical: 450 kDa

    -
    Component #1: protein, Envelope glycoprotein

    ProteinName: Envelope glycoprotein / a.k.a: gp120, gp41 / Oligomeric Details: trimer
    Details: The spike consists of 3 copies of gp120 and gp41 ecto domain to form a trimer
    Recombinant expression: No
    MassExperimental: 450 kDa
    SourceSpecies: Simian immunodeficiency virus / virus

    +
    Experimental details

    -
    Sample preparation

    Sample solutionBuffer solution: PBS
    Support film200 mesh Quantifoil R2/1 copper grid
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Vitrification instrument: Home made plunger

    -
    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM300FEG/ST / Date: Aug 30, 2004 / Details: Minimum tilt angle was -70
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 43200 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 4000 - 6000 nm
    Specimen HolderHolder: Gatan 626 cryoholder / Model: GATAN LIQUID NITROGEN / Tilt Angle: 70 - 70 deg.
    CameraDetector: TVIPS TEMCAM-F224 (2k x 2k)

    -
    Image acquisition

    Image acquisitionNumber of digital images: 80

    -
    Image processing

    ProcessingMethod: subtomogram averaging
    Details: The tomographic tilt angle increment was determined by cosine rule, i.e., ~2-3 degrees increment around low tilt angles and <1 degree increment in the high tilt angles. Average number of tilts used in the 3D reconstructions: 80. Average tomographic tilt angle increment: 2.
    3D reconstructionAlgorithm: Weighted backprojection and 3d alignment and averaging
    Software: Protomo / Resolution: 32 A / Resolution method: Estimated first node in the CTF
    Details: The resolution of the final averaged map, determined by Fourier shell correlation (based on a cutoff value of 0.5) is 2.5 nm and, after low pass filtering to the estimated first node in the contrast transfer function, 3.2 nm.

    -
    Atomic model buiding

    Modeling #1Software: Chimera / Refinement protocol: rigid body
    Details: The gp120 core and 2F5 and 4E10 peptides structure were fittted by manual docking using program chimera and then applied 3-fold symmetry around Z axis.
    Input PDB model: 2BF1, 1TJI, 1TZG
    Chain ID: 2BF1_A, 1TJI_P, 1TZG_P

    +
    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