Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - PDB-3c6d: The pseudo-atomic structure of dengue immature virus -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: PDB / ID: 3c6d
    TitleThe pseudo-atomic structure of dengue immature virus
    DescriptorPolyprotein, prM
    KeywordsVIRUS / icosahedral virion / Helicase / Hydrolase / Nucleotide-binding / RNA replication / Transmembrane / ATP-binding / Capsid protein / Cleavage on pair of basic residues / Endoplasmic reticulum / Envelope protein / Glycoprotein / Metal-binding / Multifunctional enzyme / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / Ribonucleoprotein / RNA-binding / RNA-directed RNA polymerase / Secreted / Serine protease / Transcription / Transcription regulation / Transferase / Viral nucleoprotein / icosahedral virus
    Specimen sourceDengue virus 2 Thailand/16681/84 / virus
    Dengue virus 2 / virus
    MethodElectron microscopy (12.5 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsLi, L.
    CitationScience, 2008, 319, 1830-1834

    Science, 2008, 319, 1830-1834 StrPapers
    The flavivirus precursor membrane-envelope protein complex: structure and maturation.
    Long Li / Shee-Mei Lok / I-Mei Yu / Ying Zhang / Richard J Kuhn / Jue Chen / Michael G Rossmann

    DateDeposition: Feb 4, 2008 / Release: Apr 8, 2008 / Last modification: Feb 2, 2010

    -
    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-5102
    • 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: Polyprotein
    B: Polyprotein
    C: Polyprotein
    D: prM
    E: prM
    F: prM

    159 kDa, 6 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    159,4996
    Polyers159,4996
    Non-polymers00
    Water0

    Omokage search
    #1
    A: Polyprotein
    B: Polyprotein
    C: Polyprotein
    D: prM
    E: prM
    F: prM
    x 60
    complete icosahedral assembly / 9.57 MDa, 360 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    9,569,947360
    Polyers9,569,947360
    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: Polyprotein
    B: Polyprotein
    C: Polyprotein
    D: prM
    E: prM
    F: prM
    x 5
    icosahedral pentamer / 797 kDa, 30 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    797,49630
    Polyers797,49630
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: Polyprotein
    B: Polyprotein
    C: Polyprotein
    D: prM
    E: prM
    F: prM
    x 6
    icosahedral 23 hexamer / 957 kDa, 36 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    956,99536
    Polyers956,99536
    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) / Polyprotein / Source: Dengue virus 2 Thailand/16681/84 (gene. exp.) / References: UniProt: O11875
    #2polypeptide(L) / prM / Source: Dengue virus 2 (gene. exp.) / References: UniProt: P14337

    +
    Experimental details

    -
    Experiment

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

    -
    Sample preparation

    Assembly of specimenName: DENGUE-2 IMMATURE PARTICLE / Aggregation state: PARTICLE
    Details: THE SAMPLES WERE PRODUCED BY ADDING AMMONIUM CHLORIDE TO THE MEDIA IN THE LATE INFECTION STAGE
    Details of the virusVirus host category: VERTEBRATES / Virus host growth cell: C6/36 / Virus host species: homo sapiens / Virus isolate: STRAIN / Virus type: immature virion

    -
    Electron microscopy imaging

    MicroscopyMicroscope model: PHILLIPS CM300
    Electron gunElectron source: FIELD EMISSION GUN
    Electron lensMode: BRIGHT FIELD / Calibrated magnification: 33000 X / Nominal defocus max: 364 nm / Nominal defocus min: 1662 nm / Cs: 2 mm
    Specimen holderTemperature: 1 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    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 reconstructionResolution: 12.5 A
    Atomic model buildingMethod: SEE PRIMARY CITATION / Ref protocol: RIGID BODY / Ref space: REAL
    Target criteria: USE PROGRAM EMFIT, SEARCH FOR POSTION WHERE ATOMS OCCUPY MOST EM DENSITY PEAKS
    Number of atoms included #LASTProtein: 1413 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1413

    +
    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