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    - EMDB-5044: RNA polymerase structure : Structural survey of large protein com... -

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    Basic information

    Entry
    Database: EMDB / ID: 5044
    TitleRNA polymerase structure : Structural survey of large protein complexes in Desulfovibrio vulgaris Hildenborough (DvH)
    KeywordsRNA polymerase / Desulfovibrio vulgaris / DvH / transcription
    SampleRNA polymerase from Desulfovibrio vulgaris Hildenborough
    SourceDesulfovibrio vulgaris str. hildenborough / bacteria
    Map dataRNA polymerase structure from Desulfovibrio vulgaris Hildenborough
    Methodsingle particle reconstruction, at 19 A resolution
    AuthorsHan B-G / Dong M / Liu H / Camp L / Geller J / Singer M / Hazen TC / Choi M / Witkowska HE / Ball DA / Typke D / Downing KH / Shatsky M / Brenner SE / Chandonia J-M / Biggin MD / Glaeser RM
    CitationProc. Natl. Acad. Sci. U.S.A., 2009, 106, 16580-16585

    Proc. Natl. Acad. Sci. U.S.A., 2009, 106, 16580-16585 StrPapers
    Survey of large protein complexes in D. vulgaris reveals great structural diversity.
    Bong-Gyoon Han / Ming Dong / Haichuan Liu / Lauren Camp / Jil Geller / Mary Singer / Terry C Hazen / Megan Choi / H Ewa Witkowska / David A Ball / Dieter Typke / Kenneth H Downing / Maxim Shatsky / Steven E Brenner / John-Marc Chandonia / Mark D Biggin / Robert M Glaeser

    DateDeposition: Jan 9, 2009 / Header (metadata) release: Jan 21, 2009 / Map release: Sep 4, 2009 / Last update: Jan 9, 2009

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1.8
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 1.8
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_5044.map.gz (map file in CCP4 format, 5789 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    114 pix
    3.18 A/pix
    = 362.52 A
    114 pix
    3.18 A/pix
    = 362.52 A
    114 pix
    3.18 A/pix
    = 362.52 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 3.18 A
    Density
    Contour Level:1.77 (by author), 1.8 (movie #1):
    Minimum - Maximum-2.69486141 - 18.4408989
    Average (Standard dev.)0E-8 (0.9999997)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions114114114
    Origin000
    Limit113113113
    Spacing114114114
    CellA=B=C: 362.52002 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z3.183.183.18
    M x/y/z114114114
    origin x/y/z0.0000.0000.000
    length x/y/z362.520362.520362.520
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-20-28-19
    NX/NY/NZ415638
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS114114114
    D min/max/mean-2.69518.441-0.000

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    Supplemental data

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    Sample components

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    Entire RNA polymerase from Desulfovibrio vulgaris Hildenborough

    EntireName: RNA polymerase from Desulfovibrio vulgaris Hildenborough
    Number of components: 6 / Oligomeric State: dimer
    MassTheoretical: 885 kDa / Experimental: 885 kDa

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    Component #1: protein, RNA polymerase

    ProteinName: RNA polymerase / Oligomeric Details: dimer / Recombinant expression: No
    MassTheoretical: 885 kDa / Experimental: 885 kDa
    SourceSpecies: Desulfovibrio vulgaris str. hildenborough / bacteria
    Source (natural)Location in cell: cytoplasmic

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.03 mg/ml / Buffer solution: 10 mM HEPES buffer / pH: 7
    Support filmcarbon-coated and glow-discharged 300 mesh copper grid
    StainingThree microliter of 2% w/v uranyl acetate stain was applied to the EM grid for 1 min.
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 4000EX / Date: Mar 3, 2008
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 400 kV / Electron dose: 17 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 40000 X (nominal), 40000 X (calibrated)
    Astigmatism: objective lens astigmatism was corrected at 60,000 times magnification
    Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 2000 nm
    Specimen HolderHolder: Side entry room T / Model: OTHER / Temperature: 293 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 33 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 8
    Details: The images were scanned with a resolution of 6.35 micro m per pixel and later averaged 2 fold in each direction.

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 21420 / Applied symmetry: C2 (2 fold cyclic)
    3D reconstructionAlgorithm: Refinement based on an initial model / Software: SPIDER / CTF correction: Each particle / Resolution: 19 A / Resolution method: FSC 0.5

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