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    Yorodumi
    - EMDB-1595: 20S RNA editing complex of Trypanosoma brucei -

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    Basic information

    Entry
    Database: EMDB / ID: 1595
    Title20S RNA editing complex of Trypanosoma brucei
    KeywordsRNA editing / Trypanosoma brucei
    Sample20S RNA editing complex of Trypanosoma bucei
    SourceTrypanosoma brucei / eukaryote / trypanosome /
    Map data3D map of the 20S RNA editing complex of Trypanosoma brucei
    Methodsingle particle reconstruction, at 22 A resolution
    AuthorsGolas MM / Boehm C / Sander B / Effenberger K / Brecht M / Stark H / Goeringer HU
    CitationEMBO J., 2009, 28, 766-778

    EMBO J., 2009, 28, 766-778 StrPapers
    Snapshots of the RNA editing machine in trypanosomes captured at different assembly stages in vivo.
    Monika M Golas / Cordula Böhm / Bjoern Sander / Kerstin Effenberger / Michael Brecht / Holger Stark / H Ulrich Göringer

    DateDeposition: Jan 26, 2009 / Header (metadata) release: Feb 25, 2009 / Map release: Jan 27, 2011 / Last update: Jan 26, 2009

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.0419
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 0.0419
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1595.map.gz (map file in CCP4 format, 1025 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    64 pix
    5.7 A/pix
    = 364.8 A
    64 pix
    5.7 A/pix
    = 364.8 A
    64 pix
    5.7 A/pix
    = 364.8 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 5.7 A
    Density
    Contour Level:0.0419 (by emdb), 0.0419 (movie #1):
    Minimum - Maximum-0.65175891 - 1.61760938
    Average (Standard dev.)0.00520643 (0.06710754)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions646464
    Origin000
    Limit636363
    Spacing646464
    CellA=B=C: 364.8 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z5.75.75.7
    M x/y/z646464
    origin x/y/z0.0000.0000.000
    length x/y/z364.800364.800364.800
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-17-17-200
    NX/NY/NZ123123401
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS646464
    D min/max/mean-0.6521.6180.005

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    Supplemental data

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    Sample components

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    Entire 20S RNA editing complex of Trypanosoma bucei

    EntireName: 20S RNA editing complex of Trypanosoma bucei / Details: 0.8 +/- 0.08MDa / Number of components: 1
    MassExperimental: 800 kDa

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    Component #1: cellular-component, 20S RNA editing complex

    Cellular-componentName: 20S RNA editing complex / a.k.a: editosome / Oligomeric Details: monomer / Recombinant expression: No
    SourceSpecies: Trypanosoma brucei / eukaryote / trypanosome /
    Source (natural)Organelle: mitochondria / Cell: Trypanosoma brucei

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    VitrificationInstrument: NONE / Cryogen name: NITROGEN

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200FEG
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Illumination mode: SPOT SCAN
    LensImaging mode: BRIGHT FIELD
    Specimen HolderHolder: eucentric / Model: GATAN LIQUID NITROGEN

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    Image processing

    ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
    3D reconstructionResolution: 22 A / Resolution method: FSC 0.5

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