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    Yorodumi
    - PDB-2qzf: SCR1 of DAF from 1ojv fitted into cryoEM density -

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    Basic information

    Entry
    Database: PDB / ID: 2qzf
    TitleSCR1 of DAF from 1ojv fitted into cryoEM density
    DescriptorComplement decay-accelerating factor
    KeywordsImmune system / SCR1 of DAF from structure 1ojv fitted into cryoEM density / Blood group antigen / Complement pathway / Glycoprotein / GPI-anchor / Immune response / Innate immunity / Lipoprotein / Membrane / Sushi
    Specimen sourceHomo sapiens / human
    MethodElectron microscopy (14 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsHafenstein, S. / Bowman, V.D. / Chipman, P.R. / Bator Kelly, C.M. / Lin, F. / Medof, M.E. / Rossmann, M.G.
    CitationJ. Virol., 2007, 81, 12927-12935

    J. Virol., 2007, 81, 12927-12935 StrPapers
    Interaction of decay-accelerating factor with coxsackievirus B3.
    Susan Hafenstein / Valorie D Bowman / Paul R Chipman / Carol M Bator Kelly / Feng Lin / M Edward Medof / Michael G Rossmann

    DateDeposition: Aug 16, 2007 / Release: Oct 30, 2007 / Last modification: May 30, 2012

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    Assembly

    Deposited unit
    A: Complement decay-accelerating factor

    6.88 kDa, 1 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    6,8851
    Polyers6,8851
    Non-polymers00
    Water0

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    #1idetical with deposited unit / defined by author / Symmetry operations: (identity)x1
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    Components

    #1polypeptide(L) / Complement decay-accelerating factor / CD55 antigen / Fragment: SCR1 domain / 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: coxsackievirus B3, RD strain, complexed with decay-accelerating factor
    Aggregation state: PARTICLE
    Details: one DAF binds each binding site, one per each protomer
    ComponentName: Complement decay-accelerating factor
    Buffer solutionName: 50mM MES
    Sample preparationpH: 6 / Sample conc.: 2 mg/ml
    Specimen supportDetails: quantifoils
    VitrificationDetails: blot before plunging

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T / Date: Aug 6, 2004
    Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Electron dose: 24 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4.6 nm / Nominal defocus min: 1 nm / Cs: 2 mm
    Specimen holderTemperature: 93 K / Tilt angle min: 0 deg.
    CameraType: Kodak SO-163 film
    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: EMPFT, EM3DR
    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionResolution: 14 A
    Atomic model buildingSoftware name: EMPFT, EM3DR
    Number of atoms included #LASTProtein: 479 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 479

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