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Proteomic characterization of archaeal ribosomes reveals the presence of novel archaeal-specific ribosomal proteins
by single particle reconstruction, at 25 A resolution
#1: Surface view with section colored by density value, Surface level: 0.55, Made by UCSF CHIMERA
#2: Surface view colored by height, Surface level: 0.55, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1796 |
|---|---|
| Title | Proteomic characterization of archaeal ribosomes reveals the presence of novel archaeal-specific ribosomal proteins |
| Map | This is a 50S subunit of P.aerophilum Ribosome |
| Sample | Pyrobaculum aerophilum 50S ribosomal subunit |
| Keywords |  archaea, ribosome, 50S, translation, ribosomal proteins |
| Authors | Marquez V, Froehlich T, Armache J-P, Sohmen D, Doenhoefer A, Berninghausen O, Thomm M, Beckmann R, Arnold GJ, Wilson DN |
| Date | Deposition: 2010-09-28, Header release: 2011-04-08, Map release: 2011-04-08, Last update: 2012-10-24 |
| 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 height, 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 | J. Mol. Biol., Vol. 405, Issue 5, Page 1215-32, Year 2011 |
|---|---|
| Title | Proteomic characterization of archaeal ribosomes reveals the presence of novel archaeal-specific ribosomal proteins. |
| Authors | Viter Márquez, Thomas Fröhlich, Jean-Paul Armache, Daniel Sohmen, Alexandra Dönhöfer, Aleksandra Mikolajka, Otto Berninghausen, Michael Thomm, Roland Beckmann, Georg J Arnold, Daniel N Wilson Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Feodor Lynen Str. 25, 81377 Munich, Germany. |
| Keywords | Archaeal Proteins (chemistry), Binding Sites, Lysine (chemistry, 56-87-1), Methylation, Nucleoside-Triphosphatase (metabolism, 3.6.1.15), Phylogeny, Proteomics, Pyrobaculum (chemistry), Ribosomal Proteins (chemistry), Ribosomes (chemistry), Sulfolobus acidocaldarius (chemistry) |
| Links | PII: S0022-2836(10)01285-4, DOI: 10.1016/j.jmb.2010.11.055, PubMed: 21134383 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1796.map ( map file in CCP4 format, 10514 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= B= C: 456.504 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 3.308 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is a 50S subunit of P.aerophilum Ribosome | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Pyrobaculum aerophilum 50S ribosomal subunit |
|---|---|
| Number of Components | 1 |
| Oligomeric State | One ribosomal subunit |
| Theoretical Mass | 1.5MDa |
| Mass-estimation Method | Sedimentation |
| Experimental Mass | 1.5MDa |
| Component #1: ribosome-prokaryote - 50S of P.aerophilum | |
| Scientific name | Pyrobaculum aerophilum 50S ribosomal subunit |
| Common Name | 50S of P.aerophilum |
| Theoretical Mass | 1.5 MDa |
| Experimental Mass | 1.5 MDa |
| Scientific Name of Species | Pyrobaculum aerophilum |
| NCBI taxonomy | 13773 |
| Prokaryote | LSU 50S |
| Recombinant expression | No |
 Experiment | |
| Sample Preparation | |
| Staining | Cryo-EM |
|---|---|
| Specimen State | particle |
| Buffer | Details: 20 mM Hepes pH 7.5, 10 mM Mg(OAc)2, 30 mM NH4OAc, 4 mM beta-Mercaptoethanol pH: 7.5 |
| Vitrification | |
| Method | Blot for 10 seconds before plunging, use 2 layers of filter paper |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Vitrobot |
| Humidity | 100 |
| Instrument | FEI VITROBOT |
| Imaging | |
| Microscope | FEI TECNAI 12 |
| Electron Gun | |
| Electron Source | LAB6 |
| Accelerating Voltage | 120 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 90000, Calibrated: 90000 |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1000 nm - 4500 nm |
| Specimen Holder | |
| Holder | Single tilt cryo holder |
| Model | GATAN LIQUID NITROGEN |
| Camera | |
| Detector | Eagle 2k CCD |
| Image Acquisition | |
| Number of Digital Images | 99 |
| Sampling Size | 3.308 |
| Details | Data collected on CCD |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | Projection Matching |
| Software | SPIDER |
| CTF Correction | Wiener filter on 3D volumes |
| Resolution By Author | 25 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 9183 |
| Atomic Model Fitting | |
| Model #0 | |
| Details | Rigid-body fit into the density using UCSF Chimera built-in "Fit in Map" |
| Software | UCSF Chimera |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| PDB Entry ID | 1FFK |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1796.xml (7.4 KB) | ||
|---|---|---|---|
| Map data | emd_1796.map.gz (881.1 KB) | ||
| Images |  emd1796.png (470.1 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1796 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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