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    Yorodumi
    - PDB-3epf: CryoEM structure of poliovirus receptor bound to poliovirus type 2 -

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    Basic information

    Entry
    Database: PDB / ID: 3epf
    TitleCryoEM structure of poliovirus receptor bound to poliovirus type 2
    DescriptorPoliovirus receptor
    Protein VP1
    Protein VP2
    Protein VP4
    Protein VP3
    KeywordsVIRAL PROTEIN / CD155 structure Immunoglobulin Superfamily / poliovirus capsid jelly role / Cell adhesion / Cell membrane / Glycoprotein / Host-virus interaction / Immunoglobulin domain / Membrane / Receptor / Secreted / Transmembrane
    Specimen sourceHomo sapiens / human
    Poliovirus type 2 / virus
    MethodElectron microscopy (9 A resolution)
    AuthorsZhang, P. / Mueller, S. / Morais, M.C. / Bator, C.M. / Bowman, V.D. / Hafenstein, S. / Wimmer, E. / Rossmann, M.G.
    CitationProc. Natl. Acad. Sci. U.S.A., 2008, 105, 18284-18289

    Proc. Natl. Acad. Sci. U.S.A., 2008, 105, 18284-18289 StrPapers
    Crystal structure of CD155 and electron microscopic studies of its complexes with polioviruses.
    Ping Zhang / Steffen Mueller / Marc C Morais / Carol M Bator / Valorie D Bowman / Susan Hafenstein / Eckard Wimmer / Michael G Rossmann

    DateDeposition: Sep 29, 2008 / Release: Nov 11, 2008 / Last modification: May 11, 2016

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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-1563
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    Assembly

    Deposited unit
    R: Poliovirus receptor
    1: Protein VP1
    2: Protein VP2
    4: Protein VP4
    3: Protein VP3
    hetero molecules

    117 kDa, 7 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    117,2277
    Polyers116,5755
    Non-polymers6522
    Water4,882271

    Omokage search
    #1
    R: Poliovirus receptor
    1: Protein VP1
    2: Protein VP2
    4: Protein VP4
    3: Protein VP3
    hetero molecules
    x 60
    complete icosahedral assembly / 7.03 MDa, 420 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    7,033,596420
    Polyers6,994,470300
    Non-polymers39,126120
    Water4,324240
    / Symmetry operations: (point symmetry)x60
    Download / Omokage search
    #2idetical with deposited unit in distinct coordinate / icosahedral asymmetric unit / Symmetry operations: (point symmetry)x1
    #3
    R: Poliovirus receptor
    1: Protein VP1
    2: Protein VP2
    4: Protein VP4
    3: Protein VP3
    hetero molecules
    x 5
    icosahedral pentamer / 586 kDa, 35 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    586,13335
    Polyers582,87325
    Non-polymers3,26010
    Water36020
    / Symmetry operations: (point symmetry)x5
    #4
    R: Poliovirus receptor
    1: Protein VP1
    2: Protein VP2
    4: Protein VP4
    3: Protein VP3
    hetero molecules
    x 6
    icosahedral 23 hexamer / 703 kDa, 42 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    703,36042
    Polyers699,44730
    Non-polymers3,91312
    Water43224
    / 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

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    Polypeptide(L) , 5 types, 5 molecules R1243

    #1polypeptide(L) / Poliovirus receptor / Nectin-like protein 5, Necl-5 / Fragment: Poliovirus receptor CD155 D1D2 / Mutation: N105D, N120S, N188Q, N218Q, N237S / Source: Homo sapiens (gene. exp.) / References: UniProt: P15151
    #2polypeptide(L) / Protein VP1 / Source: Poliovirus type 2 (gene. exp.) / References: UniProt: P06210
    #3polypeptide(L) / Protein VP2 / Source: Poliovirus type 2 (gene. exp.) / References: UniProt: P06210
    #4polypeptide(L) / Protein VP4 / Source: Poliovirus type 2 (gene. exp.) / References: UniProt: P06210
    #5polypeptide(L) / Protein VP3 / Source: Poliovirus type 2 (gene. exp.) / References: UniProt: P06210

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    Non-polymers , 3 types, 273 molecules

    #6ChemComp-SC4 / 1[2-CHLORO-4-METHOXY-PHENYL-OXYMETHYL]-4-[2,6-DICHLORO-PHENYL-OXYMETHYL]-BENZENE
    #7ChemComp-MYR / MYRISTIC ACID
    #8ChemComp-HOH / water

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY

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    Processing

    Image selectionSoftware name: EMfit
    3D reconstructionResolution: 9 A / Nominal pixel size: 2.69 A/pix / Actual pixel size: 2.66 A/pix
    Atomic model buildingSoftware name: EMfit / Ref space: REAL
    Number of atoms included #LASTProtein: 8152 / Nucleic acid: 0 / Ligand: 38 / Solvent: 271 / Total: 8461

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