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Ribosome dynamics and tRNA movement as visualized by time-resolved electron cryomicroscopy
by single particle reconstruction, at 9 A resolution
#1: Surface view with section colored by density value, Surface level: 40, Made by UCSF CHIMERA
#2: Surface view colored by height, Surface level: 40, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1724 |
|---|---|
| Title | Ribosome dynamics and tRNA movement as visualized by time-resolved electron cryomicroscopy |
| Map | Substate of E. coli 70S-fMetVal-tRNAVal post-translocation complex at 18 degrees C |
| Sample | Substate of E. coli 70S-fMetVal-tRNAVal post-translocation complex at 18 degrees C |
| Keywords |  Ribosome, translation, translocation, tRNA |
| Authors | Fischer N, Konevega AL, Wintermeyer W, Rodnina MV, Stark H |
| Date | Deposition: 2010-04-30, Header release: 2010-05-13, Map release: 2011-05-06, 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: 40, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 40, 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 | Nature, Vol. 466, Issue 7304, Page 329-33, Year 2010 |
|---|---|
| Title | Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy. |
| Authors | Niels Fischer, Andrey L Konevega, Wolfgang Wintermeyer, Marina V Rodnina, Holger Stark 3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. |
| Keywords | Cryoelectron Microscopy, Escherichia coli, Kinetics, Models, Molecular, Molecular Conformation, Movement, Protein Biosynthesis, RNA, Transfer (genetics, 9014-25-9), Ribosome Subunits, Large, Bacterial (chemistry), Ribosome Subunits, Small, Bacterial (chemistry), Ribosomes (chemistry), Temperature, Thermodynamics, Time Factors |
| Links | DOI: 10.1038/nature09206, PubMed: 20631791 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1724.map ( map file in CCP4 format, 13502 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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: 359.04 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 1.87 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Substate of E. coli 70S-fMetVal-tRNAVal post-translocation complex at 18 degrees C | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Substate of E. coli 70S-fMetVal-tRNAVal post-translocation complex at 18 degrees C |
|---|---|
| Number of Components | 3 |
| Theoretical Mass | 2.5MDa |
| Component #1: ribosome-prokaryote - E. coli 70S | |
| Scientific name | Ribosome |
| Common Name | E. coli 70S |
| Theoretical Mass | 2.5 MDa |
| Scientific Name of Species | Escherichia coli
|
| NCBI taxonomy | 562 |
| Prokaryote | ALL |
| Recombinant expression | No |
| Component #2: nucleic-acid - peptidyl tRNA | |
| Scientific name | fMetVal-tRNAVal |
| Common Name | peptidyl tRNA |
| Theoretical Mass | 0.025 MDa |
| Scientific Name of Species | Escherichia coli |
| NCBI taxonomy | 562 |
| Class | T-RNA |
| Structure | DOUBLE HELIX |
| Synthetic | No |
| Component #3: nucleic-acid - mRNA | |
| Scientific name | m022 mRNA |
| Common Name | mRNA |
| Details | Coding sequence AUGGUU |
| Scientific Name of Species | synthetic construct |
| NCBI taxonomy | 32630 |
| Class | RNA |
| Structure | SINGLE STRANDED |
| Synthetic | Yes |
 Experiment | |
| Sample Preparation | |
| Specimen State | particle |
|---|---|
| Buffer | Details: 50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine pH: 7.5 |
| Vitrification | |
| Method | Manual blotting for about 2 seconds |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Custom-built CEVS. Dew-point temperature (temperature on the grid) adjusted to 18 degrees C |
| Humidity | 75 |
| Instrument | HOMEMADE PLUNGER |
| Temperature | 77 Kelvin |
| Imaging | |
| Microscope | FEI/PHILIPS CM200FEG |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 160 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | SPOT SCAN |
| Lens | |
| Magnification | Nominal: 161000, Calibrated: 162740 |
| Astigmatism | Objective lens astigmatism was corrected at 200,000 times magnification |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 500 nm - 2000 nm |
| Specimen Holder | |
| Holder | Eucentric |
| Model | GATAN LIQUID NITROGEN |
| Temperature | 77 K |
| Camera | |
| Detector | 4k CCD camera (TVIPS) |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | Projection matching |
| Software | IMAGIC, custom, Spider |
| CTF Correction | Local |
| Resolution By Author | 9 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 26429 |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1724.xml (7.8 KB) | ||
|---|---|---|---|
| Map data | emd_1724.map.gz (25 MB) | ||
| Images |  image1724.png (203.9 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1724 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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