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Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
by single particle reconstruction, at 11.7 A resolution
#1: Surface view with section colored by density value, Surface level: 0.0003, Made by UCSF CHIMERA
#2: Surface view colored by height, Surface level: 0.0003, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-1s1h, PDB-1s1i, PDB-1trj, Surface level: 0.0003, Made by UCSF CHIMERA
#4: Simplified surface model with fitted atomic model: PDB-1s1h, Made by Jmol
#5: Simplified surface model with fitted atomic model: PDB-1s1i, Made by Jmol
#6: Simplified surface model with fitted atomic model: PDB-1trj, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1067 |
|---|---|
| Title | Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. |
| Map | map |
| Sample | Ribosomal 80S-eEF2-sordarin complex from S. cerevisiae |
| Authors | Spahn CM, Frank J |
| Date | Deposition: 2004-01-05, Header release: 2004-01-06, Map release: 2005-01-06, 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: 0.0003, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 0.0003, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-1s1h, PDB-1s1i, PDB-1trj, Surface level: 0.0003, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-1s1h, Made by Jmol #5: Simplified surface model with fitted atomic model: PDB-1s1i, Made by Jmol #6: Simplified surface model with fitted atomic model: PDB-1trj, 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 | EMBO J., Vol. 23, Issue 5, Page 1008-19, Year 2004 |
|---|---|
| Title | Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. |
| Authors | Christian M T Spahn, Maria G Gomez-Lorenzo, Robert A Grassucci, Rene Jørgensen, Gregers R Andersen, Roland Beckmann, Pawel A Penczek, Juan P G Ballesta, Joachim Frank Wadsworth Center, Health Research Inc., Howard Hughes Medical Institute, Albany, NY 12201-0509, USA. <> |
| Keywords |  Antifungal Agents (pharmacology), Cryoelectron Microscopy, Crystallography, X-Ray, Indenes, Models, Molecular, Movement, Nucleic Acid Conformation, Peptide Elongation Factor 2 (chemistry), Protein Binding, Protein Structure, Quaternary, Protein Structure, Tertiary, Protein Subunits (genetics), RNA Transport, RNA, Transfer (chemistry, 9014-25-9), Ribosomes (chemistry), Saccharomyces cerevisiae (chemistry), sordarin (11076-17-8) |
| Links | PubMed: 14976550, DOI: 10.1038/sj.emboj.7600102, PMC: PMC380967 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1067.map ( map file in CCP4 format, 7813 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | float (32-bit) | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 366.25 A , B = 366.25 A , C = 366.25 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 2.93 A , Y = 2.93 A , Z = 2.93 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | map | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Ribosomal 80S-eEF2-sordarin complex from S. cerevisiae |
|---|---|
| Number of Components | 2 |
| Theoretical Mass | 3.2 MDa |
| Component #1: ribosome-eukaryote - 80S ribosome | |
| Scientific name | 80S ribosome |
| Scientific Name of Species | Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
|
| Common Name of Species | Baker's yeast |
| Eukaryote | ALL |
| Recombinant expression | No |
| Component #2: protein - eEF2 | |
| Scientific name | eEF2 |
| Scientific Name of Species | Saccharomyces cerevisiae (NCBI Taxonomy: 4932) |
| Common Name of Species | Baker's yeast |
| Recombinant expression | No |
 Experiment | |
| Sample Preparation | |
| Specimen State | particle |
|---|---|
| Vitrification | |
| Cryogen Name | ETHANE |
| Imaging | |
| Microscope | FEI TECNAI F20 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 15 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 50000 X, Calibrated: 52000 X |
| Astigmatism | 100,000 X magnification |
| Nominal Cs | 2.0 mm |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder | |
| Holder | Oxford, cryo-transfer 3500 ( GATAN LIQUID NITROGEN ) |
| Tilt Angle | 0 degrees - 0 degrees |
| Temperature | 93 Kelvin |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Number of Digital Images | 86 |
| Quant Bit Number | 12 |
| Scanner | ZEISS SCAI |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | back projection |
| Software | SPIDER |
| CTF Correction | defocus group volumes |
| Resolution By Author | 11.7 |
| Resolution Method | FSC at 0.5 cut-off |
| Fitted Coordinate | |
| PDB entry ID | |
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