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    - PDB-1m11: structural model of human decay-accelerating factor bound to echo... -

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    Basic information

    Entry
    Database: PDB / ID: 1m11
    Titlestructural model of human decay-accelerating factor bound to echovirus 7 from cryo-electron microscopy
    Descriptordecay-accelerating factor/coat protein VP1/coat protein VP2/coat protein VP3
    KeywordsVirus/Receptor / decay-accelerating factor / SCR / Icosahedral virus / Virus-Receptor COMPLEX
    Specimen sourceHomo sapiens / human
    Human echovirus 7 / virus
    MethodElectron microscopy (16 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsHe, Y. / Lin, F. / Chipman, P.R. / Bator, C.M. / Baker, T.S. / Shoham, M. / Kuhn, R.J. / Medof, M.E. / Rossmann, M.G.
    CitationProc. Natl. Acad. Sci. U.S.A., 2002, 99, 10325-10329

    Proc. Natl. Acad. Sci. U.S.A., 2002, 99, 10325-10329 StrPapers
    Structure of decay-accelerating factor bound to echovirus 7: a virus-receptor complex.
    Yongning He / Feng Lin / Paul R Chipman / Carol M Bator / Timothy S Baker / Menachem Shoham / Richard J Kuhn / M Edward Medof / Michael G Rossmann

    DateDeposition: Jun 17, 2002 / Release: Aug 28, 2002 / 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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    Assembly

    Deposited unit
    R: decay-accelerating factor
    1: COAT PROTEIN VP1
    2: COAT PROTEIN VP2
    3: COAT PROTEIN VP3

    113 kDa, 4 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    113,4084
    Polyers113,4084
    Non-polymers00
    Water0

    Omokage search
    #1
    R: decay-accelerating factor
    1: COAT PROTEIN VP1
    2: COAT PROTEIN VP2
    3: COAT PROTEIN VP3
    x 60
    complete icosahedral assembly / 6.8 MDa, 240 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    6,804,454240
    Polyers6,804,454240
    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
    R: decay-accelerating factor
    1: COAT PROTEIN VP1
    2: COAT PROTEIN VP2
    3: COAT PROTEIN VP3
    x 5
    icosahedral pentamer / 567 kDa, 20 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    567,03820
    Polyers567,03820
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    R: decay-accelerating factor
    1: COAT PROTEIN VP1
    2: COAT PROTEIN VP2
    3: COAT PROTEIN VP3
    x 6
    icosahedral 23 hexamer / 680 kDa, 24 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    680,44524
    Polyers680,44524
    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) / decay-accelerating factor / Fragment: four SCR domains 1 to 4 / Source: Homo sapiens (gene. exp.) / References: UniProt: P08174
    #2polypeptide(L) / COAT PROTEIN VP1 / Source: Human echovirus 7 (gene. exp.) / References: UniProt: Q914E0
    #3polypeptide(L) / COAT PROTEIN VP2 / Source: Human echovirus 7 (gene. exp.) / References: UniProt: Q914E0
    #4polypeptide(L) / COAT PROTEIN VP3 / Source: Human echovirus 7 (gene. exp.) / References: UniProt: Q914E0

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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: human decay-accelerating factor, HUMAN ECHOVIRUS 7 COAT PROTEINS
    Aggregation state: PARTICLE
    Details: This structure is modeled based on cryo-EM density at 16A resolution.
    Buffer solutionName: tris buffer pH7.5
    Sample preparationpH: 7.5 / Sample conc.: 8 mg/ml
    VitrificationDetails: SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T / Date: Sep 10, 2001
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1660 e/A2
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Nominal defocus max: 4200 nm / Nominal defocus min: 1800 nm
    Specimen holderTemperature: 120 K

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    Processing

    Image selectionSoftware name: EMFIT
    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionMethod: PFT / Resolution: 16 A / Nominal pixel size: 3.11 A/pix / CTF correction method: CTF correction of each micrograph
    Details: The echovirus 7 structure is unknown, the model used here is from coxsackievirus B3 (1COV) and echovirus 1 (1EV1).The DAF receptor model is from 1g40. Only CA coordinates are presented in the entry.
    Atomic model buildingSoftware name: EMFIT / Ref space: REAL
    Least-squares processHighest resolution: 16 A
    Refine hist #LASTHighest resolution: 16 A
    Number of atoms included #LASTProtein: 1013 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1013

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