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    - EMDB-1435: Functional architecture of RNA polymerase I. -

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    Basic information

    Entry
    Database: EMDB / ID: 1435
    TitleFunctional architecture of RNA polymerase I.
    SampleS. cerevisiae RNA polymerase I
    SourceSaccharomyces cerevisiae / yeast / Budding yeast /
    Map dataThis is the final reconstruction of RNA polymerase I in ccp4 format.
    Methodsingle particle reconstruction, at 11.9 A resolution
    AuthorsKuhn C-D / Geiger SR / Baumli S / Gartmann M / Gerber J / Jennebach S / Mielke T / Tschochner H / Beckmann R / Cramer P
    CitationCell, 2007, 131, 1260-1272

    Cell, 2007, 131, 1260-1272 StrPapers
    Functional architecture of RNA polymerase I.
    Claus-D Kuhn / Sebastian R Geiger / Sonja Baumli / Marco Gartmann / Jochen Gerber / Stefan Jennebach / Thorsten Mielke / Herbert Tschochner / Roland Beckmann / Patrick Cramer

    DateDeposition: Sep 27, 2007 / Header (metadata) release: Sep 27, 2007 / Map release: Jan 8, 2008 / Last update: Sep 27, 2007

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.22
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 0.22
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1435.map.gz (map file in CCP4 format, 6751 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)X (Row.)Y (Col.)
    120 pix
    1.23 A/pix
    = 147.6 A
    120 pix
    1.23 A/pix
    = 147.6 A
    120 pix
    1.23 A/pix
    = 147.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.23 A
    Density
    Contour Level:0.512, 0.22 (movie #1):
    Minimum - Maximum-1.60931 - 3.05404
    Average (Standard dev.)0.0329902 (0.252014)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderYXZ
    Dimensions120120120
    Origin-60-60-59
    Limit595960
    Spacing120120120
    CellA=B=C: 147.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.231.231.23
    M x/y/z120120120
    origin x/y/z0.0000.0000.000
    length x/y/z147.600147.600147.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-60-60-59
    NX/NY/NZ120120120
    MAP C/R/S213
    start NC/NR/NS-60-60-59
    NC/NR/NS120120120
    D min/max/mean-1.6093.0540.033

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    Supplemental data

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    Sample components

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    Entire S. cerevisiae RNA polymerase I

    EntireName: S. cerevisiae RNA polymerase I / Oligomeric State: monomeric / Number of components: 1
    MassTheoretical: 600 kDa / Experimental: 600 kDa

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    Component #1: protein, RNA polymerase I

    ProteinName: RNA polymerase I / a.k.a: DNA-dependant RNA polymerase I / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 600 kDa / Experimental: 600 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / Budding yeast /
    Strain: GPY2
    Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / / Vector: pAS22
    Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: Yeast
    External referencesGene Ontology: GO: 0005736

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.1 mg/ml
    Buffer solution: 60mM ammonium sulfate, 5mM HEPES pH 7.8, 1mM magnesium chloride, 0.1mM zinc chloride
    pH: 7.8
    Support filmCarbon holey grids
    StainingVitrification
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 95 % / Details: Vitrification instrument: Vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F30 / Date: Mar 20, 2006
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: OTHER
    LensMagnification: 39000 X (nominal) / Imaging mode: BRIGHT FIELD
    Specimen HolderHolder: Eucentric / Model: OTHER / Temperature: 100 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionScanner: PRIMESCAN / Bit depth: 16 / Details: Heidelberg Drum Scanner

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 46056 / Details: Quantifoil / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Projection matching / Software: SPIDER / Resolution: 11.9 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Refinement protocol: rigid body
    Details: Protocol: rigid body. 1WCM (lacking Rpb4/7 and the foot domain) was fitted by manual docking using program O.
    Input PDB model: 1WCM

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