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    Yorodumi
    - EMDB-1753: YEAST RNA POLYMERASE III -

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    Basic information

    Entry
    Database: EMDB / ID: 1753
    TitleYEAST RNA POLYMERASE III
    KeywordsTranscription / RNA polymerase / tRNA
    SampleRNA polymerase III
    SourceSaccharomyces cerevisiae / yeast / Baker's Yeast /
    Map dataRNA-Polymerase III in its free form
    Methodsingle particle reconstruction, at 21 A resolution
    AuthorsVannini A / Ringel R / Kusser AG / Berninghausen O / Kassavetis GA / Cramer P
    CitationCell, 2010, 143, 59-70

    Cell, 2010, 143, 59-70 StrPapers
    Molecular basis of RNA polymerase III transcription repression by Maf1.
    Alessandro Vannini / Rieke Ringel / Anselm G Kusser / Otto Berninghausen / George A Kassavetis / Patrick Cramer

    DateDeposition: Jun 30, 2010 / Header (metadata) release: Jul 23, 2010 / Map release: Oct 8, 2010 / Last update: Jun 30, 2010

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.0035
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 0.0035
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1753.map.gz (map file in CCP4 format, 2849 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    90 pix
    3.31 A/pix
    = 297.9 A
    90 pix
    3.31 A/pix
    = 297.9 A
    90 pix
    3.31 A/pix
    = 297.9 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 3.31 A
    Density
    Contour Level:0.0035 (by author), 0.0035 (movie #1):
    Minimum - Maximum-0.00569051 - 0.253301
    Average (Standard dev.)0.00280515 (0.0138798)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions909090
    Origin000
    Limit898989
    Spacing909090
    CellA=B=C: 297.9 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z3.313.313.31
    M x/y/z909090
    origin x/y/z0.0000.0000.000
    length x/y/z297.900297.900297.900
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-100-100-100
    NX/NY/NZ200200200
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS909090
    D min/max/mean-0.0060.2530.003

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    Supplemental data

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    Sample components

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    Entire RNA polymerase III

    EntireName: RNA polymerase III / Details: The sample was monodisperse / Number of components: 1 / Oligomeric State: Monomeric
    MassTheoretical: 700 kDa / Experimental: 700 kDa / Measured by: Native Mass Spectrometry

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    Component #1: protein, RNA polymerase III

    ProteinName: RNA polymerase III / a.k.a: RNA polymerase III / Oligomeric Details: Monomeric / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 700 kDa / Experimental: 700 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's Yeast /
    Strain: NZ-16
    Source (engineered)Expression System: Saccharomyces cerevisiae / yeast /
    Source (natural)Location in cell: Nucleus

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.1 mg/ml
    Buffer solution: 20mM Hepes pH 7.8, 50 mM Ammonium Sulfate, 0.1 mM MgCl2, 0.01 mM ZnCl2, 5mM DTT
    pH: 7.8
    Support filmQuantifoil R3/3 2nm carbon pre-coated holey grids
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 184 K / Humidity: 95 % / Details: Vitrification instrument: Vitrobot, FEI

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: OTHER
    LensImaging mode: OTHER
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 20480 / Applied symmetry: C1 (asymmetric)
    3D reconstructionResolution: 21 A / Resolution method: FSC 0.5

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