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    - PDB-1yxn: Pseudo-atomic model of a fiberless isometric variant of bacteriop... -

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    Basic information

    Entry
    Database: PDB / ID: 1yxn
    TitlePseudo-atomic model of a fiberless isometric variant of bacteriophage phi29
    DescriptorMajor head protein
    KeywordsVirus / phi29 / capsid / icosahedral virus capsid / hk97 fold / phage / bacterial immuno-globulin / BIG2 / Icosahedral virus
    Specimen sourceBacillus phage phi29 / virus / image: Bacillus subtilis
    MethodElectron microscopy (7.9 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsMorais, M.C. / Choi, K.H. / Koti, J.S. / Chipman, P.R. / Anderson, D.L. / Rossmann, M.G.
    CitationMol. Cell, 2005, 18, 149-159

    Mol. Cell, 2005, 18, 149-159 StrPapers
    Conservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29.
    Marc C Morais / Kyung H Choi / Jaya S Koti / Paul R Chipman / Dwight L Anderson / Michael G Rossmann

    DateDeposition: Feb 22, 2005 / Release: Apr 26, 2005 / 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-1116
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    • Simplified surface model + fitted atomic model
    • EMDB-1120
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    Assembly

    Deposited unit
    A: Major head protein
    B: Major head protein
    C: Major head protein

    92 kDa, 3 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    91,9683
    Polyers91,9683
    Non-polymers00
    Water0

    Omokage search
    #1
    A: Major head protein
    B: Major head protein
    C: Major head protein
    x 60
    complete icosahedral assembly / 5.52 MDa, 180 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    5,518,084180
    Polyers5,518,084180
    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: Major head protein
    B: Major head protein
    C: Major head protein
    x 5
    icosahedral pentamer / 460 kDa, 15 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    459,84015
    Polyers459,84015
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: Major head protein
    B: Major head protein
    C: Major head protein
    x 6
    icosahedral 23 hexamer / 552 kDa, 18 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    551,80818
    Polyers551,80818
    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) / Major head protein / Late protein Gp8 / Source: Bacillus phage phi29 (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: Fiberless isometric phi29 capsid / Aggregation state: PARTICLE
    ComponentName: The capsid protein assembles a T=3 icosahedral virus shell.
    Details: The virus particle is a protein shell with icosahedral symmetry. To generate the complete icosahedral particle, apply the following 59 matrices to the three chains in the icosahedral asymmetric unit, and combine with the original coordinates of the icosahedral asymmetric unit:
    Details of the virusVirus host category: Bacteria / Virus host growth cell: Bacillus subtilus / Virus host species: Bacillus subtilus / Virus type: bacteriophage
    Buffer solutionName: tris-HCL
    Sample preparationpH: 7.8 / Sample conc.: 1 mg/ml
    Specimen supportDetails: electron microscopy grid - in vitreous ice
    VitrificationDetails: frozen in liquid ethane

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI/PHILIPS CM200FEG/ST
    Electron gunElectron source: Field emmission gun / Accelerating voltage: 200 kV
    Electron lensNominal magnification: 38000 X / Cs: 2 mm
    Specimen holderTemperature: 100 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: KODAK SO163 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: Situs (colores)
    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionMethod: 3D reconstructions were calculated using the Fourier-Bessel method. Initial orientations were found via common-lines, improved using model based polar Fourier transform methods, and finally refined by minimizing the vector difference between between structure factors calculated from a particle image and those from a central section of the Fourier transform of the model.
    Resolution: 7.9 A / Nominal pixel size: 1.8421 A/pix
    CTF correction method: Inverse of CTF was applied to images. Both phases and amplitudes were corrected.
    Details: Software used included P3DR (3D reconstructions), PFT (initial orientation improvement), and POR (final orientation refinement.
    Atomic model buildingMethod: 6D search for each symmetry related molecule in the icosahedral asymmetric unit
    Software name: Situs (colores) / Ref protocol: rigid body / Ref space: REAL
    Target criteria: rigid body refinement in real space against laplacian filtered EM density, using the program COLORES in the package SITUS. Each molecule in the T=3 asymmetric unit was refined separately.
    Number of atoms included #LASTProtein: 1080 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1080

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