Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - PDB-1z8y: Mapping the E2 Glycoprotein of Alphaviruses -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: PDB / ID: 1z8y
    TitleMapping the E2 Glycoprotein of Alphaviruses
    DescriptorSpike glycoprotein E1
    Spike glycoprotein E2
    Capsid protein C (E.C.3.4.21.-)
    KeywordsVirus / icosahedral enveloped virus / Icosahedral virus
    Specimen sourceSindbis virus / virus
    MethodElectron microscopy (9 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsMukhopadhyay, S. / Zhang, W. / Gabler, S. / Chipman, P.R. / Strauss, E.G. / Strauss, J.H. / Baker, T.S. / Kuhn, R.J. / Rossmann, M.G.
    CitationStructure, 2006, 14, 63-73

    Structure, 2006, 14, 63-73 StrPapers
    Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses.
    Suchetana Mukhopadhyay / Wei Zhang / Stefan Gabler / Paul R Chipman / Ellen G Strauss / James H Strauss / Timothy S Baker / Richard J Kuhn / Michael G Rossmann

    DateDeposition: Mar 31, 2005 / Release: Feb 7, 2006 / Last modification: Feb 24, 2009

    -
    Structure visualization

    Movie
    • Biological unit as complete icosahedral assembly
    • Imaged by Jmol
    • Download
    • Biological unit as icosahedral pentamer
    • Imaged by Jmol
    • Download
    • Biological unit as icosahedral 23 hexamer
    • Imaged by Jmol
    • Download
    • Deposited structure unit
    • Imaged by Jmol
    • Download
    • Simplified surface model + fitted atomic model
    • EMDB-1121
    • 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: Spike glycoprotein E1
    B: Spike glycoprotein E1
    C: Spike glycoprotein E1
    D: Spike glycoprotein E1
    E: Spike glycoprotein E1
    F: Spike glycoprotein E1
    G: Spike glycoprotein E1
    H: Spike glycoprotein E1
    I: Spike glycoprotein E1
    J: Spike glycoprotein E2
    K: Spike glycoprotein E1
    L: Spike glycoprotein E2
    M: Spike glycoprotein E1
    N: Spike glycoprotein E2
    O: Spike glycoprotein E1
    P: Spike glycoprotein E2
    Q: Capsid protein C
    R: Capsid protein C
    S: Capsid protein C
    T: Capsid protein C

    258 kDa, 20 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    258,38520
    Polyers258,38520
    Non-polymers00
    Water0

    Omokage search
    #1
    A: Spike glycoprotein E1
    B: Spike glycoprotein E1
    C: Spike glycoprotein E1
    D: Spike glycoprotein E1
    E: Spike glycoprotein E1
    F: Spike glycoprotein E1
    G: Spike glycoprotein E1
    H: Spike glycoprotein E1
    I: Spike glycoprotein E1
    J: Spike glycoprotein E2
    K: Spike glycoprotein E1
    L: Spike glycoprotein E2
    M: Spike glycoprotein E1
    N: Spike glycoprotein E2
    O: Spike glycoprotein E1
    P: Spike glycoprotein E2
    Q: Capsid protein C
    R: Capsid protein C
    S: Capsid protein C
    T: Capsid protein C
    x 60
    complete icosahedral assembly / 15.5 MDa, 1200 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    15,503,1051200
    Polyers15,503,1051200
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x60
    Download / Omokage search
    #2idetical with deposited unit in distinct coordinate / icosahedral asymmetric unit / Symmetry operations: (point symmetry)x1
    #3
    A: Spike glycoprotein E1
    B: Spike glycoprotein E1
    C: Spike glycoprotein E1
    D: Spike glycoprotein E1
    E: Spike glycoprotein E1
    F: Spike glycoprotein E1
    G: Spike glycoprotein E1
    H: Spike glycoprotein E1
    I: Spike glycoprotein E1
    J: Spike glycoprotein E2
    K: Spike glycoprotein E1
    L: Spike glycoprotein E2
    M: Spike glycoprotein E1
    N: Spike glycoprotein E2
    O: Spike glycoprotein E1
    P: Spike glycoprotein E2
    Q: Capsid protein C
    R: Capsid protein C
    S: Capsid protein C
    T: Capsid protein C
    x 5
    icosahedral pentamer / 1.29 MDa, 100 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,291,925100
    Polyers1,291,925100
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: Spike glycoprotein E1
    B: Spike glycoprotein E1
    C: Spike glycoprotein E1
    D: Spike glycoprotein E1
    E: Spike glycoprotein E1
    F: Spike glycoprotein E1
    G: Spike glycoprotein E1
    H: Spike glycoprotein E1
    I: Spike glycoprotein E1
    J: Spike glycoprotein E2
    K: Spike glycoprotein E1
    L: Spike glycoprotein E2
    M: Spike glycoprotein E1
    N: Spike glycoprotein E2
    O: Spike glycoprotein E1
    P: Spike glycoprotein E2
    Q: Capsid protein C
    R: Capsid protein C
    S: Capsid protein C
    T: Capsid protein C
    x 6
    icosahedral 23 hexamer / 1.55 MDa, 120 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,550,310120
    Polyers1,550,310120
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x6
    PAUidetical with deposited unit in distinct coordinate / icosahedral asymmetric unit, std point frame / Symmetry operations: (transform to point frame)x1

    -
    Components

    #1polypeptide(L) / Spike glycoprotein E1 / Fragment: E1 ectodomain domains I+II, residues 1-290 / Source: Sindbis virus (gene. exp.) / References: UniProt: P03316
    #2polypeptide(L) / Spike glycoprotein E1 / Fragment: E1 ectodomain domain III, residues 295-383 / Source: Sindbis virus (gene. exp.) / References: UniProt: P03316
    #3polypeptide(L) / Spike glycoprotein E1 / Fragment: E1 transmembrane region, residues 409-439 / Source: Sindbis virus (gene. exp.) / References: UniProt: P03316
    #4polypeptide(L) / Spike glycoprotein E2 / Fragment: E2 transmembrane region, residues 363-398 / Source: Sindbis virus (gene. exp.) / References: UniProt: P11259
    #5polypeptide(L) / Capsid protein C / coat protein C / Fragment: Capsid protein, residues 114-264 / Source: Sindbis virus (gene. exp.) / References: UniProt: P03316, EC: 3.4.21.-

    +
    Experimental details

    -
    Experiment

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

    -
    Sample preparation

    Assembly of specimenName: E2-N318Q Sindbis virus / Aggregation state: PARTICLE
    Component

    Assembly id: 1 / Details: APPLY 60 ICOSHEDRAL SYMMETRY OPERATIONS AS MATRICES TO OBTAIN THE WHOLE COMPLEX / Go id: 0005198

    NameIDIpr id
    Spike glycoprotein E1, E1 ectodomain domains I+II1IPR002548
    Spike glycoprotein E1, E1 ectodomain domain III2IPR002548
    Spike glycoprotein E1, E1 transmembrane region3IPR002548
    Spike glycoprotein E2, E2 transmembrane region4IPR000936
    Capsid protein C, residues 114-2645
    Details of the virus

    Ictvdb id: 00.073.0.01.001 / Virus host growth cell: BHK / Virus isolate: STRAIN / Virus type: Virion

    Entity assembly idIDVirus host category
    11eukaryotic virus
    22eukaryotic viru
    33eukaryotic virus
    44eukaryotic virus
    Buffer solutionName: 50 mM Tris-Cl, 200 mM NaCl, 0.1 mM EDTA
    Sample preparationpH: 7.4
    Specimen supportDetails: See Pletnev et al. (2001) Cell 105:127-136 for experimental details on sample preparation

    -
    Electron microscopy imaging

    MicroscopyMicroscope model: FEI/PHILIPS CM200FEG
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1800 e/A2 / Illumination mode: flood beam low dose
    Electron lensMode: bright field / Nominal magnification: 38000 X / Nominal defocus max: 2580 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
    Specimen holderTemperature: 93.15 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: KODAK SO163 FILM
    Details: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON MICROSCOPY DATA.
    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

    -
    Processing

    Image selectionSoftware name: EMFIT
    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionMethod: cross-common lines / Resolution: 9 A / Actual pixel size: 1.785 A/pix
    CTF correction method: Fourier transform of each image was modified
    Atomic model buildingSoftware name: EMFIT / Ref protocol: rigid body / Ref space: REAL
    Number of atoms included #LASTProtein: 18071 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 18071

    +
    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