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    Yorodumi
    - EMDB-2132: Cryo-electron tomography averaged map of microtubule doublet 2-8 ... -

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    Basic information

    Entry
    Database: EMDB / ID: 2132
    TitleCryo-electron tomography averaged map of microtubule doublet 2-8 in the distal/central region of Chlamydomonas flagella
    Keywordsaxoneme / dynein / Chlamydomonas / microtubule doublet / flagella
    SampleOuter doublets 2-8 of Chlamydomonas flagella in the distal/central region
    SourceChlamydomonas reinhardtii / plant / green algae
    Map dataReconstruction of the average of outer doublets 2-8 from Chlamydomonas flagella in the distal/central region.
    Methodsubtomogram averaging, at 36.8 A resolution
    AuthorsBui KH / Yagi T / Yamamoto R / Kamiya R / Ishikawa T
    CitationJ. Cell Biol., 2012, 198, 913-925

    J. Cell Biol., 2012, 198, 913-925 StrPapers
    Polarity and asymmetry in the arrangement of dynein and related structures in the Chlamydomonas axoneme.
    Khanh Huy Bui / Toshiki Yagi / Ryosuke Yamamoto / Ritsu Kamiya / Takashi Ishikawa

    DateDeposition: Jun 11, 2012 / Header (metadata) release: Jun 13, 2012 / Map release: Sep 12, 2012 / Last update: Jun 11, 2012

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_2132.map.gz (map file in CCP4 format, 31251 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    200 pix
    7.25 A/pix
    = 1450. A
    200 pix
    7.25 A/pix
    = 1450. A
    200 pix
    7.25 A/pix
    = 1450. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 7.25 A
    Density
    Contour Level:1 (by author), 1 (movie #1):
    Minimum - Maximum-4.212183 - 8.90901089
    Average (Standard dev.)-5E-8 (1)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions200200200
    Origin000
    Limit199199199
    Spacing200200200
    CellA=B=C: 1450 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z7.257.257.25
    M x/y/z200200200
    origin x/y/z0.0000.0000.000
    length x/y/z1450.0001450.0001450.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-32-32-32
    NX/NY/NZ646464
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS200200200
    D min/max/mean-4.2128.909-0.000

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    Supplemental data

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    Sample components

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    Entire Outer doublets 2-8 of Chlamydomonas flagella in the distal/centra...

    EntireName: Outer doublets 2-8 of Chlamydomonas flagella in the distal/central region
    Details: Flagella were purified from Chlamydomonas / Number of components: 1

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    Component #1: cellular-component, flagellum

    Cellular-componentName: flagellum / a.k.a: axoneme, cilia / Recombinant expression: No
    SourceSpecies: Chlamydomonas reinhardtii / plant / green algae / Strain: c137 (mt+)
    Source (natural)Organelle: flagella / Location in cell: distal part of the flagellum

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    Experimental details

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    Sample preparation

    Sample solutionSpecimen conc.: 2 mg/ml
    Buffer solution: 30 mM Hepes, pH 7.4, 5 mM MgSO4, 1 mM DTT, 0.5 mM EDTA, 25 mM KCl and 0.5% (wt/vol) polyethylene glycol (MW 20,000)
    pH: 7.4
    Support film300 mesh Quantifoil Holey Carbon copper grid R2/1
    VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 110 K / Humidity: 90 % / Method: Offset -3, Blot 3s, Drain time 0s

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20 / Date: Nov 26, 2010
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 60 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 27500 X (nominal), 19303 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 4000 - 6000 nm / Energy filter: Gatan Tridiem / Energy window: 0-20 eV
    Specimen HolderHolder: Gatan 626 / Model: GATAN LIQUID NITROGEN / Tilt Angle: -60 - 60 deg. / Temperature: 98 K ( 93 - 118 K)
    CameraDetector: GATAN ULTRASCAN 1000 (2k x 2k)

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    Image acquisition

    Image acquisitionNumber of digital images: 3770 / Bit depth: 16

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    Image processing

    ProcessingMethod: subtomogram averaging
    Details: R-weighted backprojection using IMOD with fiducial markers. Average number of tilts used in the 3D reconstructions: 61. Average tomographic tilt angle increment: 2.
    3D reconstructionAlgorithm: subtomogram averaging / Software: IMOD, BSOFT, SPIDER, TOM, package, Matlab / Resolution: 36.8 A / Resolution method: FSC 0.5

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