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    - PDB-1p58: Complex Organization of Dengue Virus Membrane Proteins as Reveale... -

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    Basic information

    Entry
    Database: PDB / ID: 1p58
    TitleComplex Organization of Dengue Virus Membrane Proteins as Revealed by 9.5 Angstrom Cryo-EM reconstruction
    DescriptorMajor envelope protein E/Envelope glycoprotein M
    KeywordsVirus / FLAVIVIRUS / FLAVIVIRIDAE / DENGUE VIRUS / GLYCOPROTEIN E FROM TICK-BORNE ENCEPHALITIS VIRUS / MEMBRANE PROTEIN M / CRYO-EM / Icosahedral virus
    Specimen sourceDengue virus 2 Puerto Rico/PR159-S1/1969 / virus
    MethodElectron microscopy (9.5 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsZhang, W. / Chipman, P.R. / Corver, J. / Johnson, P.R. / Zhang, Y. / Mukhopadhyay, S. / Baker, T.S. / Strauss, J.H. / Rossmann, M.G. / Kuhn, R.J.
    CitationNat. Struct. Biol., 2003, 10, 907-912

    primary. Nat. Struct. Biol., 2003, 10, 907-912 StrPapers
    Visualization of membrane protein domains by cryo-electron microscopy of dengue virus.
    Wei Zhang / Paul R Chipman / Jeroen Corver / Peter R Johnson / Ying Zhang / Suchetana Mukhopadhyay / Timothy S Baker / James H Strauss / Michael G Rossmann / Richard J Kuhn

    #1. Cell(Cambridge,Mass.), 2002, 108, 717-725
    Structure of Dengue Virus: Implications for Flaviviruses Organization, Maturation and Fusion
    Kuhn, R.J. / Zhang, W. / Rossmann, M.G. / Pletnev, S.V. / Corver, J. / Lenches, E. / Jones, C.T. / Mukhopadhyay, S. / Chipman, P.R. / Strauss, E.G. / Baker, T.S. / Strauss, J.H.

    #2. Nature, 1995, 375, 291-298
    The envelope glycoprotein from tick-borne encephalitis virus at 2 A resolution
    Rey, F.A. / Heinz, F.X. / Mandl, C. / Kunz, C. / Harrison, S.C.

    #3. Nature, 1995, 375, 275-276
    Virology. When it's better to lie low.
    Kuhn, R.J. / Rossmann, M.G.

    #4. Microbiol.Mol.Biol.Rev., 1999, 63, 862-922
    Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs
    Baker, T.S. / Olson, N.H. / Fuller, S.D.

    DateDeposition: Apr 25, 2003 / Release: Nov 4, 2003 / Last modification: Mar 2, 2011

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    Structure visualization

    Movie
    • 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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    Assembly

    Deposited unit
    A: Major envelope protein E
    B: Major envelope protein E
    C: Major envelope protein E
    D: Envelope protein M
    E: Envelope protein M
    F: Envelope protein M

    188 kDa, 6 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    188,3716
    Polyers188,3716
    Non-polymers00
    Water0

    Omokage search
    #1
    A: Major envelope protein E
    B: Major envelope protein E
    C: Major envelope protein E
    D: Envelope protein M
    E: Envelope protein M
    F: Envelope protein M
    x 60
    complete icosahedral assembly / 11.3 MDa, 360 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    11,302,239360
    Polyers11,302,239360
    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: Major envelope protein E
    B: Major envelope protein E
    C: Major envelope protein E
    D: Envelope protein M
    E: Envelope protein M
    F: Envelope protein M
    x 5
    icosahedral pentamer / 942 kDa, 30 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    941,85330
    Polyers941,85330
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: Major envelope protein E
    B: Major envelope protein E
    C: Major envelope protein E
    D: Envelope protein M
    E: Envelope protein M
    F: Envelope protein M
    x 6
    icosahedral 23 hexamer / 1.13 MDa, 36 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,130,22436
    Polyers1,130,22436
    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) / Major envelope protein E / Source: Dengue virus 2 Puerto Rico/PR159-S1/1969 (gene. exp.) / References: UniProt: P12823
    #2polypeptide(L) / Envelope protein M / Source: Dengue virus 2 Puerto Rico/PR159-S1/1969 (gene. exp.) / References: UniProt: P12823

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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 specimenName: DENGUE VIRUS / Aggregation state: PARTICLE
    Details of the virusVirus host category: INVERTEBRATES / Virus host growth cell: mosquito C6/36 / Virus host species: Aedes aegypti / Virus isolate: STRAIN / Virus type: VIRION
    Buffer solutionName: 50 mM TRIS, 75 mM NaCl, 1 mM EDTA
    Sample preparationpH: 7.6 / Sample conc.: 20 mg/ml
    Specimen supportDetails: Concentration is given in PFU/ML
    VitrificationDetails: SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI/PHILIPS CM200T / Date: Jun 27, 2000
    Electron gunElectron source: SCHOTTKY FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2700 e/A2 / Illumination mode: FLOOD BEAM LOW DOSE
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 48 nm / Nominal defocus min: 8 nm / Cs: 2 mm
    Specimen holderTemperature: 87 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: KODAK SO163 FILM

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    Processing

    Image selectionSoftware name: EMFIT / Number of particles: 1691
    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionMethod: FOURIER-BESSEL METHOD / Resolution: 9.5 A / Nominal pixel size: 2.8 A/pix
    CTF correction method: each viral image was CTF corrected before reconstruction, based on the following equation: F(corr)=F(obs)/[|CTF|+wiener*(1-|CTF|)]
    Details: THE RECONSTRUCTION WAS COMPUTED FROM 1691 DENGUE VIRUS IMAGES THAT WERE SELECTED FROM 78 MICROGRAPHS. ORIENTATIONS WERE DETERMINED BY THE MODEL-BASED POLAR-FOURIER TRANSFORM METHOD (BAKER AND CHENG, 1996, J.STRUC.BIOL. 116,120-130) AND REFINED BY THE MODEL-BASED FOURIER TRANSFORM REFINEMENT PROCEDURE(http://bond.cs.ucf.edu/ComputationalBiology/Projects/POR/Home.html).
    Atomic model buildingSoftware name: EMFIT / Ref space: REAL
    Number of atoms included #LASTProtein: 1635 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1635

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