3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
YEAST RNA POLYMERASE III
by single particle reconstruction
#1: Surface view with section colored by density value, Surface level: 0.0035, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 0.0035, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1753 |
|---|---|
| Title | YEAST RNA POLYMERASE III |
| Map | RNA-Polymerase III in its free form |
| Sample | RNA polymerase III |
| Keywords |  Transcription, RNA polymerase, tRNA |
| Authors | Vannini A, Ringel R, Kusser AG, Berninghausen O, Kassavetis GA, Cramer P |
| Date | Deposition: 2010-06-30, Header release: 2010-07-23, Map release: 2010-10-08, Last update: 2010-10-08 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.0035, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 0.0035, 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 | Cell, Vol. 143, Issue 1, Page 59-70, Year 2010 |
|---|---|
| Title | Molecular basis of RNA polymerase III transcription repression by Maf1. |
| Authors | Alessandro Vannini, Rieke Ringel, Anselm G Kusser, Otto Berninghausen, George A Kassavetis, Patrick Cramer Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany. |
| Keywords | Amino Acid Sequence, MAF1 protein, S cerevisiae, Molecular Sequence Data, Multiprotein Complexes (chemistry), Promoter Regions, Genetic, RNA Polymerase III (antagonists & inhibitors, 2.7.7.-), Saccharomyces cerevisiae (chemistry), Saccharomyces cerevisiae Proteins (chemistry), Sequence Alignment, Transcription Factors (chemistry), Transcription, Genetic |
| Links | PII: S0092-8674(10)01012-3, DOI: 10.1016/j.cell.2010.09.002, PubMed: 20887893 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1753.map ( map file in CCP4 format, 2918 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 = 297.9 A , B = 297.9 A , C = 297.9 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 3.31 A , Y = 3.31 A , Z = 3.31 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | RNA-Polymerase III in its free form | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | RNA polymerase III |
|---|---|
| Number of Components | 1 |
| Oligomeric State | Monomeric |
| Theoretical Mass | 0.7 MDa |
| Details | The sample was monodisperse |
| Mass-estimation Method | Native Mass Spectrometry |
| Experimental Mass | 0.7 MDa |
| Component #1: protein - RNA polymerase III | |
| Scientific name | RNA polymerase III |
| Theoretical Mass | 0.7 MDa |
| Experimental Mass | 0.7 MDa |
| Oligomeric Details | Monomeric |
| Number of Copies | 1 |
| Scientific Name of Species | Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
|
| Common Name of Species | Baker's Yeast |
| Strain | NZ-16 |
| Recombinant expression | Yes |
| Natural Source | Cell Location: Nucleus |
| Engineered Source | Exp System: Saccharomyces cerevisiae (NCBI Taxonomy: 4932) |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 0.1 mg/ml |
|---|---|
| Specimen Support Details | Quantifoil R3/3 2nm carbon pre-coated holey grids |
| Specimen State | particle |
| Buffer | Details: 20mM Hepes pH 7.8, 50 mM Ammonium Sulfate, 0.1 mM MgCl2, 0.01 mM ZnCl2, 5mM DTT pH: 7.8 |
| Vitrification | |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Vitrobot, FEI |
| Humidity | 95 |
| Instrument | FEI VITROBOT |
| Temperature | 184 Kelvin |
| Imaging | |
| Microscope | FEI TECNAI F20 |
| Electron Gun | |
| Electron Source | LAB6 |
| Accelerating Voltage | 120 kV |
| Illumination Mode | OTHER |
| Lens | |
| Imaging Mode | OTHER |
| Specimen Holder | |
| Holder | Eucentric ( GATAN LIQUID NITROGEN ) |
| Camera | |
| Image Acquisition | |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| Single Particle | |
| Number of Projections | 20480 |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1753.xml (6.3 KB) | ||
|---|---|---|---|
| Map data | emd_1753.map.gz (2.7 MB) | ||
| Images | 1753.tif (1.5 MB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1753 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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