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    Yorodumi
    - EMDB-1316: High-resolution electron microscopy of helical specimens: a fresh... -

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    Basic information

    Entry
    Database: EMDB / ID: 1316
    TitleHigh-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus.
    SampleTobacco Mosaic Virus
    SourceTobacco mosaic virus / virus / Virus
    Map dataA 69 Angstrom section of the virus. The complete virus contains contains approximately 44 repeats of this 69 Angstrom section. The section contains 49 asymmetric units of the helical virus.Cube of 241 x 241 x 241 Angstrom
    Methodhelical reconstruction, at 4.4 A resolution
    AuthorsSachse C / Chen JZ / Coureux PD / Stroupe ME / Fandrich M / Grigorieff N
    CitationJ. Mol. Biol., 2007, 371, 812-835

    J. Mol. Biol., 2007, 371, 812-835 StrPapers
    High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus.
    Carsten Sachse / James Z Chen / Pierre-Damien Coureux / M Elizabeth Stroupe / Marcus Fändrich / Nikolaus Grigorieff

    DateDeposition: Jan 22, 2007 / Header (metadata) release: Jan 22, 2007 / Map release: Jun 25, 2007 / Last update: Jan 22, 2007

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 2
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 2
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1316.map.gz (map file in CCP4 format, 31251 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    200 pix
    1.16 A/pix
    = 232.6 A
    200 pix
    1.16 A/pix
    = 232.6 A
    200 pix
    1.16 A/pix
    = 232.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.163 A
    Density
    Contour Level:0.581, 2 (movie #1):
    Minimum - Maximum-5.16884 - 6.75695
    Average (Standard dev.)-0.0334474 (0.671369)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions200200200
    Origin-100-100-100
    Limit999999
    Spacing200200200
    CellA=B=C: 232.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.1631.1631.163
    M x/y/z200200200
    origin x/y/z0.0000.0000.000
    length x/y/z232.600232.600232.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ
    NX/NY/NZ
    MAP C/R/S123
    start NC/NR/NS-100-100-100
    NC/NR/NS200200200
    D min/max/mean-5.1696.757-0.033

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    Supplemental data

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    Sample components

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    Entire Tobacco Mosaic Virus

    EntireName: Tobacco Mosaic Virus / Number of components: 1
    MassTheoretical: 37.5 MDa

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    Component #1: virus, Tobacco mosaic virus

    VirusName: Tobacco mosaic virus / a.k.a: Virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
    MassExperimental: 37.5 MDa
    SpeciesSpecies: Tobacco mosaic virus / virus / Virus
    Source (natural)Host Species: Nicotiana tabacum / plant / / Host category: PLANTAE(HIGHER PLANTS)

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    Experimental details

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    Sample preparation

    Specimen statefilament
    Helical parametersAxial symmetry: C1 (asymmetric) / Hand: RIGHT HANDED
    Sample solutionSpecimen conc.: 2.5 mg/ml / Buffer solution: Phosphate (5mM EDTA) / pH: 7.4
    Support filmQuantifoil grid
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Method: Blot for 2 seconds before plunging / Details: Vitrification instrument: self-built model

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F30 / Date: Nov 22, 2005
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 59000 X (nominal), 60190 X (calibrated)
    Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 4500 nm
    Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
    Model: GATAN LIQUID NITROGEN / Temperature: 93 K ( 93 - 93 K)
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 6 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: helical reconstruction
    3D reconstructionAlgorithm: SIRT - iterative algebraic reconstruction methods
    Software: Spider
    CTF correction: CTFFIND and CTFTILT phase-correction and amplitude-weighting of each paritcle after Grigorieff 1998
    Resolution: 4.4 A / Resolution method: 5
    Details: Final map was calculated from the central 241x241x241 cube.

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    Atomic model buiding

    Modeling #1Software: XPLOR / Refinement protocol: flexible
    Target criteria: minimization of of least-square difference between observed and calculated densities
    Refinement space: REAL
    Details: Protocol: Torsion angle dynamics. 2TMV pdb code structure was adjusted to fit the density for residues 88-109 and refined
    Input PDB model: 2OM3
    Chain ID: A, R

    Overall bvalue: 90
    Output model

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