|Entry||Database: EMDB / ID: 5044|
|Title||RNA polymerase structure : Structural survey of large protein complexes in Desulfovibrio vulgaris Hildenborough (DvH)|
|Keywords||RNA polymerase / Desulfovibrio vulgaris / DvH / transcription|
|Sample||RNA polymerase from Desulfovibrio vulgaris Hildenborough|
|Source||Desulfovibrio vulgaris str. hildenborough / bacteria|
|Map data||RNA polymerase structure from Desulfovibrio vulgaris Hildenborough|
|Method||single particle reconstruction, at 19 Å resolution|
|Authors||Han 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|
|Citation||Proc. Natl. Acad. Sci. U.S.A., 2009, 106, 16580-16585|
Proc. Natl. Acad. Sci. U.S.A., 2009, 106, 16580-16585 Yorodumi Papers
|Date||Deposition: Jan 9, 2009 / Header (metadata) release: Jan 21, 2009 / Map release: Sep 4, 2009 / Last update: Dec 11, 2013|
Downloads & links
|File||emd_5044.map.gz (map file in CCP4 format, 5789 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 3.18 Å|
CCP4 map header:
-Entire RNA polymerase from Desulfovibrio vulgaris Hildenborough
|Entire||Name: RNA polymerase from Desulfovibrio vulgaris Hildenborough|
Number of components: 6 / Oligomeric State: dimer
|Mass||Theoretical: 885 kDa / Experimental: 885 kDa|
-Component #1: protein, RNA polymerase
|Protein||Name: RNA polymerase / Oligomeric Details: dimer / Recombinant expression: No|
|Mass||Theoretical: 885 kDa / Experimental: 885 kDa|
|Source||Species: Desulfovibrio vulgaris str. hildenborough / bacteria|
|Source (natural)||Location in cell: cytoplasmic|
|Sample solution||Specimen conc.: 0.03 mg/ml / Buffer solution: 10 mM HEPES buffer / pH: 7|
|Support film||carbon-coated and glow-discharged 300 mesh copper grid|
|Staining||Three microliter of 2% w/v uranyl acetate stain was applied to the EM grid for 1 min.|
|Vitrification||Instrument: NONE / Cryogen name: NONE|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 4000EX / Date: Mar 3, 2008|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 400 kV / Electron dose: 17 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 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 Holder||Holder: Side entry room T / Model: OTHER / Temperature: 293 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number 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.
|Processing||Method: single particle reconstruction / Number of projections: 21420 / Applied symmetry: C2 (2 fold cyclic)|
|3D reconstruction||Algorithm: Refinement based on an initial model / Software: SPIDER / CTF correction: Each particle / Resolution: 19 Å / Resolution method: FSC 0.5|
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