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    - PDB-3c6r: Low pH Immature Dengue Virus -

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    Basic information

    Entry
    Database: PDB / ID: 3c6r
    TitleLow pH Immature Dengue Virus
    DescriptorEnvelope protein
    Peptide pr
    KeywordsVIRUS / dengue / immature / prM / E / Capsid protein / Cleavage on pair of basic residues / Core protein / Endoplasmic reticulum / Envelope protein / Glycoprotein / Membrane / Secreted / Transmembrane / Virion / icosahedral virus / virus
    Specimen sourceDengue virus type 2 / virus
    MethodElectron microscopy (25 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsYu, I. / Zhang, W. / Holdway, H.A. / Li, L. / Kostyuchenko, V.A. / Chipman, P.R. / Kuhn, R.J. / Rossmann, M.G. / Chen, J.
    CitationScience, 2008, 319, 1834-1837

    Science, 2008, 319, 1834-1837 StrPapers
    Structure of the immature dengue virus at low pH primes proteolytic maturation.
    I-Mei Yu / Wei Zhang / Heather A Holdaway / Long Li / Victor A Kostyuchenko / Paul R Chipman / Richard J Kuhn / Michael G Rossmann / Jue Chen

    DateDeposition: Feb 5, 2008 / Release: Apr 22, 2008 / Last modification: Feb 2, 2010

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    Structure visualization

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    • Biological unit as complete icosahedral assembly
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    • Biological unit as icosahedral pentamer
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    • Biological unit as icosahedral 23 hexamer
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    • Deposited structure unit
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    • Simplified surface model + fitted atomic model
    • EMDB-5006
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    Assembly

    Deposited unit
    A: Envelope protein
    D: Peptide pr
    B: Envelope protein
    E: Peptide pr
    C: Envelope protein
    F: Peptide pr

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

    Omokage search
    #1
    A: Envelope protein
    D: Peptide pr
    B: Envelope protein
    E: Peptide pr
    C: Envelope protein
    F: Peptide pr
    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: Envelope protein
    D: Peptide pr
    B: Envelope protein
    E: Peptide pr
    C: Envelope protein
    F: Peptide pr
    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: Envelope protein
    D: Peptide pr
    B: Envelope protein
    E: Peptide pr
    C: Envelope protein
    F: Peptide pr
    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

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    Components

    #1polypeptide(L) / Envelope protein / Source: Dengue virus type 2 (gene. exp.) / References: UniProt: P18356
    #2polypeptide(L) / Peptide pr / Source: Dengue virus type 2 (gene. exp.) / References: UniProt: P18356

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    Experimental details

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    Experiment

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

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    Sample preparation

    Assembly of specimenAggregation state: PARTICLE

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    Electron microscopy imaging

    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: EMfit
    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionMethod: Cross-correlation in real and reciprocal space for orientation determination; Fourier-Bessel method for reconstruction.
    Resolution: 25 A / Nominal pixel size: 2.8 A/pix / Actual pixel size: 2.7 A/pix / Magnification calibration: Grating Replica EM grid
    CTF correction method: Both amplitude and phase of CTF are corrected for each boxed particle.
    Atomic model buildingSoftware name: EMfit / Ref space: REAL
    Number of atoms included #LASTProtein: 1422 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1422

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