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    Yorodumi
    - EMDB-1441: The role of the kinesin-13 neck in microtubule depolymerization. -

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    Basic information

    Entry
    Database: EMDB / ID: 1441
    TitleThe role of the kinesin-13 neck in microtubule depolymerization.
    SampleMalarial kinesin-13 motor core ADP
    SourcePlasmodium falciparum / eukaryote / Malaria /
    Map dataA realspace map of kinesin-13-bound, 15 protofilament microtubules, calculated from averaged layer line data using Fourier-Bessel synthesis
    Methodhelical reconstruction, at 20 A resolution
    AuthorsMoores CA / Hekmat-Nejad M / Sakowicz R / Milligan RA
    CitationCell Cycle, 2006, 5, 1812-1815

    Cell Cycle, 2006, 5, 1812-1815 StrPapers
    The role of the kinesin-13 neck in microtubule depolymerization.
    Carolyn A Moores / Jeremy Cooper / Mike Wagenbach / Yulia Ovechkina / Linda Wordeman / Ronald A Milligan

    DateDeposition: Oct 8, 2007 / Header (metadata) release: Oct 8, 2007 / Map release: Oct 8, 2007 / Last update: Oct 8, 2007

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    Structure visualization

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    • Surface view with section colored by density value
    • Surface level: 10
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 10
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1441.map.gz (map file in CCP4 format, 2910 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    73 pix
    4.97 A/pix
    = 362.81 A
    101 pix
    4.97 A/pix
    = 501.97 A
    101 pix
    4.97 A/pix
    = 501.97 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 4.97 A
    Density
    Contour Level:28, 10 (movie #1):
    Minimum - Maximum-37 - 48
    Average (Standard dev.)1.62657 (10.558)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions10110173
    Origin000
    Limit10010072
    Spacing10110173
    CellA: 501.97 A / B: 501.97 A / C: 362.81 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z4.974.974.97
    M x/y/z10110173
    origin x/y/z0.0000.0000.000
    length x/y/z501.970501.970362.810
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-60-60-59
    NX/NY/NZ120120120
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS10110173
    D min/max/mean-37.00048.0001.627

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    Supplemental data

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    Sample components

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    Entire Malarial kinesin-13 motor core ADP

    EntireName: Malarial kinesin-13 motor core ADP / Details: Molecular weight of kinesin motor core is 40kD
    Oligomeric State: monomeric kinesin binds to each tubulin dimer
    Number of components: 2

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    Component #1: protein, kinesin-13 motor core

    ProteinName: kinesin-13 motor core / a.k.a: pKinI / Oligomeric Details: monomer / Recombinant expression: Yes
    MassTheoretical: 40 kDa / Experimental: 40 kDa
    SourceSpecies: Plasmodium falciparum / eukaryote / Malaria /
    Source (engineered)Expression System: Escherichia coli / bacteria /

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    Component #2: protein, tubulin

    ProteinName: tubulin / Oligomeric Details: helical polymer / Recombinant expression: No
    MassTheoretical: 100 kDa / Experimental: 100 kDa
    SourceSpecies: Plasmodium falciparum / eukaryote / Malaria /
    Source (natural)Location in cell: cytoplasmic / Cell: neurone / Organ or tissue: brain

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    Experimental details

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    Sample preparation

    Specimen statefilament
    Helical parametersHand: LEFT HANDED
    Sample solutionSpecimen conc.: 3 mg/ml
    Buffer solution: 20mM Pipes, 2mM MgCl2, 1mM EGTA, 1mM DTT,5mM ADP
    pH: 6.8
    Support film400 mesh quantifoil grid 2/2
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 98 % / Method: blot for 3-4s before plunging
    Details: Vitrification instrument: plunger. vitrification performed in humidified cold room

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200FEG / Date: Aug 1, 2002
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 38000 X (nominal) / Astigmatism: objective lens astigmatism was corrected at / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 950 - 2200 nm
    Specimen HolderHolder: side entry, nitrogen cooled / Model: GATAN LIQUID NITROGEN / Temperature: 95 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 50 / Scanner: PERKIN ELMER / Sampling size: 20 microns

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    Image processing

    ProcessingMethod: helical reconstruction
    3D reconstructionAlgorithm: Fourier Bessel synthesis / Software: Phoelix / CTF correction: each microtubule / Resolution: 20 A / Resolution method: layer line phase information / Details: Final map calculated from 184 moire repeats

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