3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Conformational flexibility of RNA polymerase III during transcriptional elongation
by single particle reconstruction, at 11.5 A resolution
#1: Surface view with section colored by density value, Surface level: 0.55, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 0.55, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1802 |
|---|---|
| Authors | Fernandez-Tornero C, Bottcher B, Rashid UJ, Steuerwald U, Florchinger B, Devos DP, Lindner D, Muller CW |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.55, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 0.55, 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 | EMBO J., Vol. 29, Issue 22, Page 3762-72, Year 2010 |
|---|---|
| Title | Conformational flexibility of RNA polymerase III during transcriptional elongation. |
| Authors | Carlos Fernández-Tornero, Bettina Böttcher, Umar Jan Rashid, Ulrich Steuerwald, Beate Flörchinger, Damien P Devos, Doris Lindner, Christoph W Müller European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany. |
| Keywords |  Cryoelectron Microscopy, Models, Molecular, Protein Conformation, Protein Multimerization, Protein Structure, Tertiary, RNA Polymerase III (chemistry, 2.7.7.-), Saccharomyces cerevisiae (chemistry), Structural Homology, Protein, Transcription, Genetic |
| Links | DOI: 10.1038/emboj.2010.266, PubMed: 20967027, PMC: PMC2989110 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1802.map ( map file in CCP4 format, 23330 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||
| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
| ||||||||||||||||||||||||
| Unit Cell | A = 252 A , B = 252 A , C = 252 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 1.4 A , Y = 1.4 A , Z = 1.4 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | The map represents the RNA-polymerase III. | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | RNA Polymerase III |
|---|---|
| Number of Components | 1 |
| Oligomeric State | One complex of 17 different polypeptides |
| Theoretical Mass | 0.7 MDa |
| Details | Sample was monodisperse |
| Mass-estimation Method | Native mass spectrometry |
| Experimental Mass | 0.7 MDa |
| Component #1: protein - Pol III | |
| Scientific name | RNA polymerase III |
| Common Name | Pol III |
| Theoretical Mass | 0.7 MDa |
| Experimental Mass | 0.7 MDa |
| Oligomeric Details | Complex of 17 subunits |
| Number of Copies | 1 |
| Scientific Name of Species | Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
|
| Common Name of Species | Yeast |
| Recombinant expression | Yes |
| Natural Source | Cell Location: Nuclear |
| Engineered Source | Exp System: Saccharomyces cerevisiae (NCBI Taxonomy: 4932) |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 0.5 mg/ml |
|---|---|
| Specimen Support Details | 400 mesh copper rhodium grids coated with perforated carbon film |
| Specimen State | particle |
| Buffer | Details: 10 mM Tris-HCl pH 7.4 150 mM Ammonium sulphate 10 mM DTT pH: 7.4 |
| Vitrification | |
| Method | Blot for 15 s in controlled environment chamber before plunging |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Controlled environment, self-built |
| Humidity | 100 |
| Instrument | HOMEMADE PLUNGER |
| Imaging | |
| Microscope | FEI/PHILIPS CM200FEG |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 50000 X, |
| Astigmatism | Astigmatism was corrected at 200,000 times magnification |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1600 nm - 5000 nm |
| Specimen Holder | |
| Holder | Eucentric ( GATAN LIQUID NITROGEN ) |
| Tilt Angle | 0 degrees - 0 degrees |
| Temperature | 95 Kelvin |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | ZEISS SCAI |
| Number of Digital Images | 593 |
| Sampling Size | 7 microns |
| Quant Bit Number | 8 |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | Projection matching |
| Software | SPIDER |
| CTF Correction | Each particle |
| Details | Maps were calculated from defocus groups,and added. final combined map was amplitude corrected |
| Resolution By Author | 11.5 |
| Resolution Method | 0.5 |
| Single Particle | |
| Number of Projections | 40200 |
| Details | ca. 100000 particles were sorted into three groups according to compositional differences. The reconstruction shows the most complete species and represents ca. 48% of the particle population. |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1802.xml (8 KB) | ||
|---|---|---|---|
| Map data | emd_1802.map.gz (20.6 MB) | ||
| Images |  1802.png (139 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1802 | ||
| Movie files | |||
| movie #1 |
| ||
| movie #2 |
| ||
Top
Gallery
List
Diagram
Statistics
Documents
PDBj
EM Navigator
Detail page - EMDB-1802
Z (Sec.)
Y (Row.)
X (Col.)
Contact