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    - PDB-1upn: COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR... -

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    Entry
    Database: PDB / ID: 1upn
    TitleCOMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A
    DescriptorECHOVIRUS 11 COAT PROTEIN VP1
    ECHOVIRUS 11 COAT PROTEIN VP2
    ECHOVIRUS 11 COAT PROTEIN VP3
    ECHOVIRUS 11 COAT PROTEIN VP4
    COMPLEMENT DECAY-ACCELERATING FACTOR
    KeywordsVIRUS/RECEPTOR / COMPLEX (VIRUS COAT-IMMUNE PROTEIN) / ECHOVIRUS / PICORNAVIRUS / CD55 / DAF / VIRUS-RECEPTOR COMPLEX / ICOSAHEDRAL VIRUS
    Specimen sourceHomo sapiens / human
    HUMAN ECHOVIRUS 11 / virus
    MethodElectron microscopy (16 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsBhella, D. / Goodfellow, I.G. / Roversi, P. / Pettigrew, D. / Chaudry, Y. / Evans, D.J. / Lea, S.M.
    CitationJ. Biol. Chem., 2004, 279, 8325-8332

    J. Biol. Chem., 2004, 279, 8325-8332 StrPapers
    The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55).
    David Bhella / Ian G Goodfellow / Pietro Roversi / David Pettigrew / Yasmin Chaudhry / David J Evans / Susan M Lea

    DateDeposition: Oct 8, 2003 / Release: Jan 7, 2004 / Last modification: Feb 24, 2009

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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-1057
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    • Simplified surface model + fitted atomic model
    • EMDB-1058
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    Assembly

    Deposited unit
    A: ECHOVIRUS 11 COAT PROTEIN VP1
    B: ECHOVIRUS 11 COAT PROTEIN VP2
    C: ECHOVIRUS 11 COAT PROTEIN VP3
    D: ECHOVIRUS 11 COAT PROTEIN VP4
    E: COMPLEMENT DECAY-ACCELERATING FACTOR

    109 kDa, 5 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    109,3375
    Polyers109,3375
    Non-polymers00
    Water0

    Omokage search
    #1
    A: ECHOVIRUS 11 COAT PROTEIN VP1
    B: ECHOVIRUS 11 COAT PROTEIN VP2
    C: ECHOVIRUS 11 COAT PROTEIN VP3
    D: ECHOVIRUS 11 COAT PROTEIN VP4
    E: COMPLEMENT DECAY-ACCELERATING FACTOR
    x 60
    complete icosahedral assembly / 6.56 MDa, 300 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    6,560,243300
    Polyers6,560,243300
    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: ECHOVIRUS 11 COAT PROTEIN VP1
    B: ECHOVIRUS 11 COAT PROTEIN VP2
    C: ECHOVIRUS 11 COAT PROTEIN VP3
    D: ECHOVIRUS 11 COAT PROTEIN VP4
    E: COMPLEMENT DECAY-ACCELERATING FACTOR
    x 5
    icosahedral pentamer / 547 kDa, 25 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    546,68725
    Polyers546,68725
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: ECHOVIRUS 11 COAT PROTEIN VP1
    B: ECHOVIRUS 11 COAT PROTEIN VP2
    C: ECHOVIRUS 11 COAT PROTEIN VP3
    D: ECHOVIRUS 11 COAT PROTEIN VP4
    E: COMPLEMENT DECAY-ACCELERATING FACTOR
    x 6
    icosahedral 23 hexamer / 656 kDa, 30 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    656,02430
    Polyers656,02430
    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) / ECHOVIRUS 11 COAT PROTEIN VP1 / Source: HUMAN ECHOVIRUS 11 (gene. exp.) / References: UniProt: Q8JKE8
    #2polypeptide(L) / ECHOVIRUS 11 COAT PROTEIN VP2 / Source: HUMAN ECHOVIRUS 11 (gene. exp.) / References: UniProt: Q8JKE8
    #3polypeptide(L) / ECHOVIRUS 11 COAT PROTEIN VP3 / Source: HUMAN ECHOVIRUS 11 (gene. exp.) / References: UniProt: Q8JKE8
    #4polypeptide(L) / ECHOVIRUS 11 COAT PROTEIN VP4 / STRUCTURE OF ECHOVIRUS TYPE 11 FITTED INTO CRYO-EM ELECTRON DENSITY FOR ECHOVIRUS TYPE 12. THE EM DENSITY HAS BEEN DEPOSITED IN THE EMDB, WITH ACCESSION CODE 1057 / Source: HUMAN ECHOVIRUS 11 (gene. exp.) / References: UniProt: Q8JKE8
    #5polypeptide(L) / COMPLEMENT DECAY-ACCELERATING FACTOR / CD55 / Source: HOMO SAPIENS (gene. exp.) / References: UniProt: P08174

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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: ECHOVIRUS TYPE 12 / Aggregation state: PARTICLE
    Buffer solutionName: AMMONIUM MOLYBDATE
    Sample preparationpH: 7.4 / Sample conc.: 0.2 mg/ml
    Specimen supportDetails: HOLEY CARBON
    VitrificationDetails: LIQUID ETHANE

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    Electron microscopy imaging

    MicroscopyMicroscope model: JEOL 1200 EX II / Date: Jul 15, 2002 / Details: PARTICLES SELECTED WITH X3D
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: LOW DOSE
    Electron lensNominal magnification: 30000 X / Calibrated magnification: 29200 X / Nominal defocus max: 2000 nm / Nominal defocus min: 300 nm / Cs: 3.4 mm
    Specimen holderTemperature: 108 K
    CameraType: KODAK SO-163 FILM
    EM image scansNumber digital images: 16
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: MRC
    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionMethod: POLAR FOURIER TRANSFORM
    Details: MAP BROUGHT TO P23 CRYSTAL WITH UNIT CELL DIMENSIONS OF 599.375 599.375 599.375 90.00 90.00 90.00. MODEL FOR EV11 DOCKED ONTO EV12 EM DENSITY. 0.5 A GAP BETWEEN CD55 DOMAIN 3 AND DOMAIN 4 WAS INTRODUCED BY RIGID-BODY REFINEMENT OF DOMAIN 4 KEEPING 3 FIXED
    Atomic model buildingRef protocol: X-RAY / Ref space: REAL / Target criteria: CORRELATION COEFFICIENTS
    Least-squares processHighest resolution: 16 A
    Refine hist #LASTHighest resolution: 16 A
    Number of atoms included #LASTProtein: 7463 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 7463

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