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tmRNA translocation and MLD-loading on the ribosome: a 70S-tmRNA-EF-G complex
by single particle reconstruction, at 8.3 A resolution
#1: Surface view with section colored by density value, Surface level: 2, Made by UCSF CHIMERA
#2: Surface view colored by height, Surface level: 2, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-3j18, PDB-3j19, Surface level: 2, Made by UCSF CHIMERA
#4: Simplified surface model with fitted atomic model: PDB-3j18, Made by Jmol
#5: Simplified surface model with fitted atomic model: PDB-3j19, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5386 |
|---|---|
| Title | tmRNA translocation and MLD-loading on the ribosome: a 70S-tmRNA-EF-G complex |
| Map | Overall view of the 70S-tmRNA-SmpB-EF-G complex |
| Sample | Complex of 70S-tmRNA-SmpB-EF-G |
| Keywords |  trans-translation, MLD-loading, translocation, tmRNA, EF-G, SmpB |
| Authors | Ramrath DJF, Yamamoto H, Rother K, Wittek D, Pech M, Mielke T, Loerke J, Scheerer P, Ivanov P, Teraoka Y, Shpanchenko O, Nierhaus KH, Spahn CMT |
| Date | Deposition: 2012-01-20, Header release: 2012-02-21, Map release: 2012-04-30, Last update: 2012-04-30 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 2, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 2, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-3j18, PDB-3j19, Surface level: 2, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-3j18, Made by Jmol #5: Simplified surface model with fitted atomic model: PDB-3j19, Made by Jmol |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: output model of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | Nature, Vol. 485, Issue 7399, Page 526-9, Year 2012 |
|---|---|
| Title | The complex of tmRNA-SmpB and EF-G on translocating ribosomes. |
| Authors | David J F Ramrath, Hiroshi Yamamoto, Kristian Rother, Daniela Wittek, Markus Pech, Thorsten Mielke, Justus Loerke, Patrick Scheerer, Pavel Ivanov, Yoshika Teraoka, Olga Shpanchenko, Knud H Nierhaus, Christian M T Spahn Institut für Medizinische Physik und Biophysik, Charite - Universitätsmedizin Berlin, Ziegelstrasse 5-9, 10117 Berlin, Germany. |
| Keywords | Base Sequence, Cryoelectron Microscopy, Escherichia coli (chemistry), Fusidic Acid (metabolism, 6990-06-3), Ligands, Models, Molecular, Nucleic Acid Conformation, Peptide Elongation Factor G (chemistry), Protein Binding, Protein Biosynthesis, Protein Conformation, RNA, Bacterial (chemistry), RNA-Binding Proteins (chemistry), Ribosome Subunits (chemistry), Ribosomes (chemistry), small protein B, tmRNA |
| Links | DOI: 10.1038/nature11006, PubMed: 22622583 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5386.map ( map file in CCP4 format, 108002 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: 378 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 1.26 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Overall view of the 70S-tmRNA-SmpB-EF-G complex | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | Complex of 70S-tmRNA-SmpB-EF-G |
|---|---|
| Number of Components | 5 |
| Oligomeric State | Monomer |
| Theoretical Mass | 3MDa |
| Details | the sample was flash frozen in liquid ethane |
| Mass-estimation Method | Sedimentation |
| Experimental Mass | 3MDa |
| Component #1: ribosome-prokaryote - 70S-tmRNA-EFG | |
| Scientific name | Ribosome |
| Common Name | 70S-tmRNA-EFG |
| Theoretical Mass | 3.05 MDa |
| Experimental Mass | 3 MDa |
| Details | the complex was stalled with fusidic acid |
| Scientific Name of Species | Escherichia coli
|
| NCBI taxonomy | 562 |
| Strain | CAN20 |
| Prokaryote | ALL |
| Recombinant expression | No |
 Experiment | |
| Sample Preparation | |
| Staining | flash frozen in liquid ethane |
|---|---|
| Specimen Conc | 0.15 mg/ml |
| Specimen Support Details | Quantifoil R3-3 Cu 300 mesh with 2 nm carbon support film |
| Specimen State | particle |
| Buffer | Details: 20 mM HEPES-KOH, pH 7.6, 4.5 mM Mg(Ac)2, 150 mM NH4Ac, 4 mM b-mercaptoethanol, 2 mM spermidine, and 0.05 mM spermine pH: 7.6 |
| Vitrification | |
| Method | blot for 10 seconds before plunging |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: FEI VITROBOT |
| Humidity | 100 |
| Instrument | FEI VITROBOT |
| Temperature | 96.15 Kelvin |
| Imaging | |
| Microscope | FEI POLARA 300 |
| Date | 08-DEC-2009 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 300 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | SPOT SCAN |
| Lens | |
| Magnification | Nominal: 39000, Calibrated: 39000 |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 2000 nm - 5000 nm |
| Specimen Holder | |
| Holder | Cartridge |
| Model | GATAN HELIUM |
| Temperature | 77.15 K ( 77.15 - 81.15 K) |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | PRIMESCAN |
| Number of Digital Images | 302 |
| Sampling Size | 4.7 |
| Quant Bit Number | 16 |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | angular refinement |
| Software | Spider |
| CTF Correction | Defocus groups |
| Resolution By Author | 8.3 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 68842 |
| Atomic Model Fitting | |
| Model #0 | |
| Target Criteria | cross-correlation |
| Details | Protocol: Rigid Body |
| Software | Chimera |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| PDB Entry ID | 3R8S |
| Fitted Coordinate | |
| PDB entry ID | |
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