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    - PDB-3iy3: Variable domains of the computer generated model (WAM) of Fab 8 f... -

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    Basic information

    Entry
    Database: PDB / ID: 3iy3
    TitleVariable domains of the computer generated model (WAM) of Fab 8 fitted into the cryoEM reconstruction of the virus-Fab 8 complex
    Descriptorantibody fragment from neutralizing antibody 8
    KeywordsIMMUNE SYSTEM / cryoEM / neutralizing antibody / parvovirus / canine / feline / fab footprint
    Specimen sourceMus musculus / mammal /
    MethodElectron microscopy (11.1 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsHafenstein, S. / Bowman, V.D. / Sun, T. / Nelson, C.D. / Palermo, L.M. / Chipman, P.R. / Battisti, A.J. / Parrish, C.R. / Rossmann, M.G.
    CitationJ. Virol., 2009, 83, 5556-5566

    J. Virol., 2009, 83, 5556-5566 StrPapers
    Structural comparison of different antibodies interacting with parvovirus capsids.
    Susan Hafenstein / Valorie D Bowman / Tao Sun / Christian D S Nelson / Laura M Palermo / Paul R Chipman / Anthony J Battisti / Colin R Parrish / Michael G Rossmann

    DateDeposition: Apr 9, 2009 / Release: May 12, 2009 / Last modification: May 26, 2009

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    Assembly

    Deposited unit
    A: antibody fragment from neutralizing antibody 8 (light chain)
    B: antibody fragment from neutralizing antibody 8 (heavy chain)

    25.4 kDa, 2 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    25,3822
    Polyers25,3822
    Non-polymers00
    Water0

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

    #1polypeptide(L) / antibody fragment from neutralizing antibody 8 (light chain) / Fragment: FAb 8 / Source: Mus musculus (gene. exp.)
    #2polypeptide(L) / antibody fragment from neutralizing antibody 8 (heavy chain) / Source: Mus musculus (gene. exp.)

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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: Fab fragment from MAb 8 interacting with feline panleukopenia virus (FPV)
    Aggregation state: PARTICLE / Number of components: 2
    ComponentType: VIRUS / Synonym: FPV
    Details of the virusEmpty: NO / Enveloped: NO / Virus host category: VERTEBRATES / Virus host species: Felis catus / Virus isolate: STRAIN / Virus type: VIRION
    Sample preparationDetails: 10 mM Tris / pH: 7.5 / Sample conc.: 1 mg/ml
    VitrificationInstrument: plunger / Cryogen name: ETHANE / Temp: 120 K / Method: blot before plunging

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    Electron microscopy imaging

    EM imagingCamera length: 0 mm
    MicroscopyDate: Jan 23, 2004
    Electron gunAccelerating voltage: 300 kV / Electron dose: 25.44 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 47190 X / Nominal defocus max: 3.1 nm / Nominal defocus min: 1.8 nm
    Astigmatism: lens astigmatism was corrected at 100,000 times magnification
    Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: side mounted nitrogen cooled / Temperature: 93 K / Temperature (max): 83 K / Temperature (min): 83 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: Kodak SO-163 film
    EM image scansDetails: scanned at 7 microns and bin averaged to 14 / Number digital images: 49 / Od range: 0.9 / Sampling size: 7 microns / Scanner model: ZEISS SCAI
    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionNumber of particles: 4344
    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionMethod: common lines / Software: EMPFT EM3DR / Resolution: 11.1 A / Resolution method: FSC at 0.5 cutoff / Number of particles: 4344 / CTF correction method: robem
    Number of atoms included #LASTProtein: 1788 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1788

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