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RNA polymerase structure : Structural survey of large protein complexes in Desulfovibrio vulgaris Hildenborough (DvH)
by single particle reconstruction, at 19 A resolution
#1: Surface view with section colored by density value, Surface level: 1.8, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 1.8, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5044 |
|---|---|
| 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 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 1.8, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 1.8, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | Proc. Natl. Acad. Sci. U.S.A., Vol. 106, Issue 39, Page 16580-5, Year 2009 |
|---|---|
| Title | Survey of large protein complexes in D. vulgaris reveals great structural diversity. |
| Authors | 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 Life Sciences, Genomics, Earth Sciences, and Physical Biosciences Divisions, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA. |
| Keywords |  Bacterial Proteins (chemistry), Crystallography, X-Ray, Databases, Protein, Desulfovibrio vulgaris (chemistry), Models, Molecular, Multiprotein Complexes (chemistry), Protein Conformation |
| Links | DOI: 10.1073/pnas.0813068106, PubMed: 19805340, PMC: PMC2742403 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5044.map ( map file in CCP4 format, 5928 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 362.52 A , B = 362.52 A , C = 362.52 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 3.18 A , Y = 3.18 A , Z = 3.18 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | RNA polymerase structure from Desulfovibrio vulgaris Hildenborough | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | RNA polymerase from Desulfovibrio vulgaris Hildenborough |
|---|---|
| Number of Components | 6 |
| Oligomeric State | dimer |
| Theoretical Mass | 0.885 MDa |
| Experimental Mass | 0.885 MDa |
| Component #1: protein - RNA polymerase | |
| Scientific name | RNA polymerase |
| Theoretical Mass | 0.885 MDa |
| Experimental Mass | 0.885 MDa |
| Oligomeric Details | dimer |
| Recombinant expression | No |
| Natural Source | Cell: Desulfovibrio vulgaris Hildenborough Cell Location: cytoplasmic |
 Experiment | |
| Sample Preparation | |
| Staining | Three microliter of 2% w/v uranyl acetate stain was applied to the EM grid for 1 min. |
|---|---|
| Specimen Conc | 0.03 mg/ml |
| Specimen Support Details | carbon-coated and glow-discharged 300 mesh copper grid |
| Specimen State | particle |
| Buffer | Details: 10 mM HEPES buffer pH: 7.0 |
| Vitrification | |
| Cryogen Name | NONE |
| Instrument | NONE |
| Imaging | |
| Microscope | JEOL 4000EX |
| Date | 03-Mar-2008 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 400 kV |
| Electron Dose | 17 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 40000 X, Calibrated: 40000 X |
| Astigmatism | objective lens astigmatism was corrected at 60,000 times magnification |
| Nominal Cs | 4.1 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 600 nm - 2000 nm |
| Specimen Holder | |
| Holder | Side entry room T ( OTHER ) |
| Tilt Angle | 0 degrees - 0 degrees |
| Temperature | 293 Kelvin |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | NIKON SUPER COOLSCAN 9000 |
| Number of Digital Images | 33 |
| Sampling Size | 6.35 microns |
| Quant Bit Number | 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 |
|---|---|
| 3 D reconstruction | |
| Algorithm | Refinement based on an initial model |
| Software | SPIDER |
| CTF Correction | Each particle |
| Resolution By Author | 19 |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 21420 |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-5044.xml (7.6 KB) | ||
|---|---|---|---|
| Map data | emd_5044.map.gz (4.8 MB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5044 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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