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    - PDB-2c8i: Complex Of Echovirus Type 12 With Domains 1, 2, 3 and 4 Of Its Re... -

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    Basic information

    Entry
    Database: PDB / ID: 2c8i
    TitleComplex Of Echovirus Type 12 With Domains 1, 2, 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 / PICORNAVIRUS / DAF / VIRUS-RECEPTOR COMPLEX / ANTIGEN / BLOOD GROUP ANTIGEN / COMPLEMENT PATHWAY / GPI-ANCHOR / IMMUNE RESPONSE / INNATE IMMUNITY / LIPOPROTEIN / PLASMA / SUSHI
    Specimen sourceHomo sapiens / human
    HUMAN ECHOVIRUS 11 / virus
    MethodElectron microscopy (14 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsPettigrew, D.M. / Williams, D.T. / Kerrigan, D. / Evans, D.J. / Lea, S.M. / Bhella, D.
    CitationJ. Biol. Chem., 2006, 281, 5169-5177

    primary. J. Biol. Chem., 2006, 281, 5169-5177 StrPapers
    Structural and functional insights into the interaction of echoviruses and decay-accelerating factor.
    David M Pettigrew / David T Williams / David Kerrigan / David J Evans / Susan M Lea / David Bhella

    #1. J.Biol.Chem., 2004, 279, 8325- StrPapers
    Complex of Echovirus Type 12 with Domains 3 and 4 of its Receptor Decay Accelerating Factor (Cd55) by Cryo Electron Microscopy at 16 A
    Bhella, D. / Goodfellow, I.G. / Roversi, P. / Pettigrew, D. / Chaudry, Y. / Evans, D.J. / Lea, S.M.

    DateDeposition: Dec 5, 2005 / Release: Jan 17, 2006 / Last modification: Apr 21, 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-1182
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    • Simplified surface model + fitted atomic model
    • EMDB-1183
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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

    128 kDa, 5 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    127,9975
    Polyers127,9975
    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 / 7.68 MDa, 300 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    7,679,793300
    Polyers7,679,793300
    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 / 640 kDa, 25 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    639,98325
    Polyers639,98325
    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 / 768 kDa, 30 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    767,97930
    Polyers767,97930
    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: P29813
    #2polypeptide(L) / ECHOVIRUS 11 COAT PROTEIN VP2 / Source: HUMAN ECHOVIRUS 11 (gene. exp.) / References: UniProt: P29813
    #3polypeptide(L) / ECHOVIRUS 11 COAT PROTEIN VP3 / Source: HUMAN ECHOVIRUS 11 (gene. exp.) / References: UniProt: P29813
    #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: P29813
    #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 BOUND TO DECAY ACCELERATING FACTOR / Aggregation state: PARTICLE / Details: CRYO-NEGATIVE STAIN IMAGES. 96 FOCAL PAIRS.
    Buffer solutionName: PHOSPHATE BUFFERED SALINE
    Sample preparationpH: 7.4 / Sample conc.: 0.2 mg/ml
    Specimen supportDetails: HOLEY CARBON
    VitrificationDetails: STAINED WITH AMMONIUM MOLYBDATE PH 7.2. VITRIFIED IN LIQUID ETHANE (CRYO-NEGATIVE STAIN)

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    Electron microscopy imaging

    MicroscopyDate: Sep 1, 2004
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: LOW DOSE
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 30000 X / Calibrated magnification: 29100 X / Nominal defocus max: 2800 nm / Nominal defocus min: 600 nm / Cs: 3.4 mm
    Specimen holderTemperature: 100 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: KODAK SO163
    EM image scansNumber digital images: 192
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: EM3DR2, PFT2 / Number of particles: 1742
    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionMethod: POLAR FOURIER TRANSFORM METHOD / Resolution: 14 A / Nominal pixel size: 2.18 A/pix / Actual pixel size: 2.18 A/pix
    CTF correction method: DEFOCUS PAIR IMAGES OF INDIVIDUAL PARTICLES
    Details: THE SEQUENCE OF THE ECHOVIRUS CAPSID PROTEINS IS FROM EV11 BUT THE EM DENSITY INTO WHICH THE STRUCTURE WAS FITTED IS THAT OF EV12
    Atomic model buildingMethod: LOCAL CORRELATION / Ref protocol: LOCAL CORRELATION / Ref space: REAL / Target criteria: OPTIMAL CORRELATION
    Least-squares processHighest resolution: 14 A
    Refine hist #LASTHighest resolution: 14 A
    Number of atoms included #LASTProtein: 1091 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1091

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