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    Yorodumi
    - EMDB-1036: Structure of a fast kinesin: implications for ATPase mechanism an... -

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    Basic information

    Entry
    Database: EMDB / ID: 1036
    TitleStructure of a fast kinesin: implications for ATPase mechanism and interactions with microtubules.
    Sampleneurospora crassa kinesin monomer
    SourceNeurospora crassa / fungus / neurospora
    Map dataNeurospora crassa kinesin monomer (nK355) AMP-PNP state
    Methodhelical reconstruction, at 25 A resolution
    AuthorsKrebs A
    CitationEMBO J., 2001, 20, 6213-6225

    EMBO J., 2001, 20, 6213-6225 StrPapers
    Structure of a fast kinesin: implications for ATPase mechanism and interactions with microtubules.
    Y H Song / A Marx / J Müller / G Woehlke / M Schliwa / A Krebs / A Hoenger / E Mandelkow

    DateDeposition: Feb 27, 2003 / Header (metadata) release: Feb 27, 2003 / Map release: Feb 27, 2003 / Last update: Feb 27, 2003

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 53.068715402
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 53.068715402
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1036.map.gz (map file in CCP4 format, 3908 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    100 pix
    5.53 A/pix
    = 552.6 A
    100 pix
    5.53 A/pix
    = 552.6 A
    100 pix
    5.53 A/pix
    = 552.6 A

    Surface

    Projections

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    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 5.526 A
    Density
    Contour Level:64.5, 53.0687154 (movie #1):
    Minimum - Maximum0 - 100
    Average (Standard dev.)42.9539 (9.96501)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions100100100
    Origin000
    Limit999999
    Spacing100100100
    CellA=B=C: 552.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z5.5265.5265.526
    M x/y/z100100100
    origin x/y/z0.0000.0000.000
    length x/y/z552.600552.600552.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ
    NX/NY/NZ
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS100100100
    D min/max/mean0.000100.00042.954

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    Supplemental data

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    Sample components

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    Entire neurospora crassa kinesin monomer

    EntireName: neurospora crassa kinesin monomer / Oligomeric State: monomer / Number of components: 2

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    Component #1: protein, neurospora crassakinesin

    ProteinName: neurospora crassakinesin / a.k.a: molecular motor / Oligomeric Details: monomer / Number of Copies: 1 / Recombinant expression: Yes
    SourceSpecies: Neurospora crassa / fungus / neurospora

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    Component #2: protein, tubulin

    ProteinName: tubulin / a.k.a: microtubules / Oligomeric Details: hetero dimer / Recombinant expression: No / Number of Copies: 1
    SourceSpecies: Neurospora crassa / fungus / neurospora
    Source (natural)Location in cell: cytoplasm / Cell: neuronal cells / Organ or tissue: brain

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    Experimental details

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    Sample preparation

    Specimen statefilament
    Helical parametersAxial symmetry: C1 (asymmetric) / Hand: LEFT HANDED
    Sample solutionSpecimen conc.: 0.5 mg/ml
    Buffer solution: Pipes 20mM, 50 mM NaCl, 5mM mgcl,1mM Mg-ATP, 20um taxol.
    pH: 6.9
    Support filmholey grids
    Stainingice-embedded
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: PROPANE / Temperature: 93 K / Details: Vitrification instrument: self made

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM120T
    Electron gunElectron source: LAB6 / Accelerating voltage: 100 kV / Electron dose: 5 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 37000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 2000 nm
    Specimen HolderHolder: side entry / Model: GATAN LIQUID NITROGEN
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 18 / Scanner: ZEISS SCAI / Sampling size: 21 microns / Bit depth: 16

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    Image processing

    ProcessingMethod: helical reconstruction
    3D reconstructionAlgorithm: helical / Software: Phoelix, Suprim / Resolution: 25 A / Resolution method: FSC 0.5
    Details: Final maps from 36 averaged datasets = 18 helical tubes

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