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    Yorodumi
    - EMDB-5205: Structure of microtubule decorated with PRC1 -

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    Basic information

    Entry
    Database: EMDB / ID: 5205
    TitleStructure of microtubule decorated with PRC1
    SamplePRC1
    SourceUnidentified
    Map dataThis is an image of section of microtubule decorated with PRC1
    Methodhelical reconstruction, at 18 A resolution
    AuthorsSubramanian R / Wilson-Kubalek EM / Arthur CP / Bick MJ / Campbell EA / Darst SA / Milligan RA / Kapoor TM
    CitationCell, 2010, 142, 433-443

    Cell, 2010, 142, 433-443 StrPapers
    Insights into antiparallel microtubule crosslinking by PRC1, a conserved nonmotor microtubule binding protein.
    Radhika Subramanian / Elizabeth M Wilson-Kubalek / Christopher P Arthur / Matthew J Bick / Elizabeth A Campbell / Seth A Darst / Ronald A Milligan / Tarun M Kapoor

    DateDeposition: Jun 30, 2010 / Header (metadata) release: Sep 10, 2010 / Map release: Sep 10, 2010 / Last update: Jun 30, 2010

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 14
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 14
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_5205.map.gz (map file in CCP4 format, 11766 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    103 pix
    5.35 A/pix
    = 550.535 A
    171 pix
    5.35 A/pix
    = 913.995 A
    171 pix
    5.35 A/pix
    = 913.995 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel size
    XYZ
    EMDB info.5.3455.3455.345
    CCP4 map header5.3455.3455.345
    EM Navigator Movie #13.473.473.47
    Density
    Contour Level:2.5 (by author), 14 (movie #1):
    Minimum - Maximum-32 - 50
    Average (Standard dev.)0.847337 (10.7397)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions171171103
    Origin000
    Limit170170102
    Spacing171171103
    CellA: 913.995 A / B: 913.995 A / C: 550.535 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z5.3455.3455.345
    M x/y/z171171103
    origin x/y/z0.0000.0000.000
    length x/y/z913.995913.995550.535
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-99-99-99
    NX/NY/NZ200200200
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS171171103
    D min/max/mean-32.00050.0000.847

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    Supplemental data

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    Sample components

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    Entire PRC1

    EntireName: PRC1 / Details: Decorated microtubules / Number of components: 2

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    Component #1: protein, Microtubule

    ProteinName: Microtubule / a.k.a: PRC1 / Recombinant expression: Yes
    SourceSpecies: Unidentified

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    Experimental details

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    Sample preparation

    Specimen statefilament
    Helical parametersHand: LEFT HANDED
    VitrificationInstrument: NONE / Cryogen name: ETHANE

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20 / Date: Feb 2, 2010
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 10 e/A2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
    LensMagnification: 35000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 900 - 2000 nm
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 93 K ( 93 - 93 K)
    CameraDetector: GENERIC GATAN

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    Image acquisition

    Image acquisitionNumber of digital images: 10

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    Image processing

    ProcessingMethod: helical reconstruction
    3D reconstructionAlgorithm: Fourier Bessel inversion / Software: PHOELIX / CTF correction: CTF correction of each micrograph / Resolution: 18 A / Resolution method: Coherent phase determination

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