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    Yorodumi
    - EMDB-5330: Cryo-electron tomography reveals novel interactions and doublet-s... -

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    Basic information

    Entry
    Database: EMDB / ID: 5330
    TitleCryo-electron tomography reveals novel interactions and doublet-specific structures in the I1 dynein
    Keywordsaxoneme / molecular motor / motility regulation / flagella
    SampleCryo-electron tomography and subtomographic average (750 axonemal repeats) of isolated axonemes of wild type Chlamydomonas (CC 125, 137c), I1 dynein complex (dynein f) is bound to the doublet microtubule and is connected to neighboring structures.
    SourceChlamydomonas reinhardtii / plant / unicellular green algae
    Map dataThis is a subtomogram average of the I1 inner dynein complex in wild type Chlamydomonas flagella
    Methodsubtomogram averaging, at 39 A resolution
    AuthorsHeuser T / Barber CF / Lin J / Krell J / Rebesco M / Porter ME / Nicastro D
    CitationProc. Natl. Acad. Sci. U.S.A., 2012, 109, E2067-E2076

    Proc. Natl. Acad. Sci. U.S.A., 2012, 109, E2067-E2076 StrPapers
    Cryoelectron tomography reveals doublet-specific structures and unique interactions in the I1 dynein.
    Thomas Heuser / Cynthia F Barber / Jianfeng Lin / Jeremy Krell / Matthew Rebesco / Mary E Porter / Daniela Nicastro

    DateDeposition: Aug 10, 2011 / Header (metadata) release: Aug 11, 2011 / Map release: Jun 21, 2012 / Last update: Aug 10, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 127.5
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 127.5
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_5330.map.gz (map file in CCP4 format, 345 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    40 pix
    9.5 A/pix
    = 380. A
    40 pix
    9.5 A/pix
    = 522.5 A
    55 pix
    9.5 A/pix
    = 380. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 9.5 A
    Density
    Contour Level:127.5 (by author), 127.5 (movie #1):
    Minimum - Maximum109.59519958 - 148.88063049
    Average (Standard dev.)124.20162964 (5.68234873)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions405540
    Origin-53-21-64
    Limit-1433-25
    Spacing554040
    CellA: 380 A / B: 522.5 A / C: 380 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z9.59.59.5
    M x/y/z405540
    origin x/y/z0.0000.0000.000
    length x/y/z380.000522.500380.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-21-53-64
    NC/NR/NS554040
    D min/max/mean109.595148.881124.202

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    Supplemental data

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    Sample components

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    Entire Cryo-electron tomography and subtomographic average (750 axonemal...

    EntireName: Cryo-electron tomography and subtomographic average (750 axonemal repeats) of isolated axonemes of wild type Chlamydomonas (CC 125, 137c), I1 dynein complex (dynein f) is bound to the doublet microtubule and is connected to neighboring structures.
    Number of components: 1

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    Component #1: cellular-component, I1 dynein complex

    Cellular-componentName: I1 dynein complex / a.k.a: dynein f / Recombinant expression: No / Number of Copies: 2
    SourceSpecies: Chlamydomonas reinhardtii / plant / unicellular green algae
    Strain: CC-125, 137c
    Source (natural)Organelle: eukaryotic flagella / Cell: Chlamydomonas reinhardtii

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    Experimental details

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    Sample preparation

    Sample solutionSpecimen conc.: 1 mg/ml
    Buffer solution: 10 mM HEPES, pH 7.4, 25 mM NaCl, 4 mM MgSO4, 1 mM EGTA, 0.1 mM EDTA
    pH: 7.4
    Support filmQuantifoil holey carbon grids Cu 200 mesh R2/2
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 100 K / Method: front-side blotting for 2-3 seconds

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F30 / Date: Feb 20, 2004
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 100 e/A2 / Illumination mode: OTHER
    LensMagnification: 13500 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 6000 - 8000 nm / Energy filter: GATAN postcolumn filter GIF / Energy window: 0-20 eV
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Tilt Angle: -60 - 60 deg. / Temperature: 80 K
    CameraDetector: GENERIC GATAN (2k x 2k)

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    Image processing

    ProcessingMethod: subtomogram averaging
    Details: 750 axonemal repeats (96 nm long) from 5 tomograms (reconstructed using fiducial alignment and weighted backprojection, IMOD software, Kremer et al. 1996) were aligned and averaged using the PEET software (bio3d.colorado.edu, Nicastro et al. 2006). Average number of tilts used in the 3D reconstructions: 80. Average tomographic tilt angle increment: 1.5.
    3D reconstructionAlgorithm: fiducial alignment and weighted backprojection / Software: IMOD
    Details: Final maps were calculated by averaging 750 particles from 5 tomograms
    Resolution: 39 A / Resolution method: FSC 0.5

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