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Interactions of the release factor RF1 with the ribosome as revealed by cryo-EM.
by single particle reconstruction, at 12.8 A resolution
#1: Surface view with section colored by density value, Surface level: 20, Made by UCSF CHIMERA
#2: Surface view colored by height, Surface level: 20, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-2fvo, PDB-3dg4, Surface level: 20, Made by UCSF CHIMERA
#4: Simplified surface model with fitted atomic model: PDB-2fvo, Made by Jmol
#5: Simplified surface model with fitted atomic model: PDB-3dg4, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1184 |
|---|---|
| Title | Interactions of the release factor RF1 with the ribosome as revealed by cryo-EM. |
| Map | This is an em map of a 70s E.coli ribosome |
| Sample | Release complex bound with RF1-WT |
| Authors | Rawat U, Gao H, Zavialov A, Gursky R, Ehrenberg M, Frank J |
| Date | Deposition: 2006-01-31, Header release: 2006-01-31, Map release: 2006-05-09, Last update: 2012-10-31 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 20, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 20, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-2fvo, PDB-3dg4, Surface level: 20, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-2fvo, Made by Jmol #5: Simplified surface model with fitted atomic model: PDB-3dg4, 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 | J. Mol. Biol., Vol. 357, Issue 4, Page 1144-53, Year 2006 |
|---|---|
| Title | Interactions of the release factor RF1 with the ribosome as revealed by cryo-EM. |
| Authors | Urmila Rawat, Haixiao Gao, Andrey Zavialov, Richard Gursky, Måns Ehrenberg, Joachim Frank Howard Hughes Medical Institute, University of Michigan School of Medicine, 1150 West Medical Ctr. Drive, Ann Arbor, MI 48109, USA. |
| Keywords |  Cryoelectron Microscopy, GTP Phosphohydrolases (chemistry, 3.6.1.-), Models, Molecular, Molecular Sequence Data, Peptide Termination Factors (chemistry), Peptidyl Transferases (chemistry, 2.3.2.12), Protein Binding, Protein Biosynthesis, Protein Conformation, Ribosomes (chemistry), Thermotoga maritima (metabolism), peptide chain termination release factor 2 |
| Links | PII: S0022-2836(06)00066-0, DOI: 10.1016/j.jmb.2006.01.038, PubMed: 16476444 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1184.map ( map file in CCP4 format, 8789 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 |
| ||||||||||||||||||||||||
| Unit Cell | A= B= C: 366.6 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 2.82 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is an em map of a 70s E.coli ribosome | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Release complex bound with RF1-WT |
|---|---|
| Number of Components | 6 |
| Component #1: ribosome-prokaryote - 30S | |
| Scientific name | 30S |
| Scientific Name of Species | Escherichia coli
|
| NCBI taxonomy | 562 |
| Strain | MRE600 |
| Prokaryote | SSU 30S |
| Recombinant expression | No |
| Component #2: ribosome-prokaryote - 50S | |
| Scientific name | 50S |
| Scientific Name of Species | Escherichia coli |
| NCBI taxonomy | 562 |
| Strain | MRE600 |
| Prokaryote | LSU 50S |
| Recombinant expression | No |
| Component #3: nucleic-acid - P-site tRNA | |
| Scientific name | P-site tRNA |
| Scientific Name of Species | Escherichia coli |
| NCBI taxonomy | 562 |
| Class | RNA |
| Synthetic | No |
| Structure | OTHER |
| Component #4: nucleic-acid - E-site tRNA | |
| Scientific name | E-site tRNA |
| Scientific Name of Species | Escherichia coli |
| NCBI taxonomy | 562 |
| Synthetic | No |
| Structure | OTHER |
| Class | RNA |
| Component #5: nucleic-acid - mRNA | |
| Scientific name | mRNA |
| Scientific Name of Species | synthetic construct |
| NCBI taxonomy | 32630 |
| Synthetic | Yes |
| Class | RNA |
| Structure | DOUBLE HELIX |
| Component #6: protein - RF1 | |
| Scientific name | RF1 |
| Scientific Name of Species | Escherichia coli |
| NCBI taxonomy | 562 |
| Strain | MRE600 |
| Recombinant expression | No |
 Experiment | |
| Sample Preparation | |
| Specimen State | particle |
|---|---|
| Vitrification | |
| Method | Blot for 2 seconds before plunging |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: two sided blotting plunger |
| Humidity | 90 |
| Instrument | HOMEMADE PLUNGER |
| Temperature | 93 Kelvin |
| Imaging | |
| Microscope | FEI TECNAI F20 |
| Date | 2002-12-01 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 50000, Calibrated: 49696 |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 2000 nm - 4000 nm |
| Specimen Holder | |
| Holder | Cryo stage |
| Model | GATAN LIQUID NITROGEN |
| Tilt Angle | 0 degrees - 0 degrees |
| Temperature | 93 K |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Od Range | 1.2 |
| Scanner | ZEISS SCAI |
| Number of Digital Images | 56 |
| Sampling Size | 14 |
| Quant Bit Number | 12 |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | reference projection |
| Euler Angles Details | SPIDER: theta 15 degrees, phi 15 degrees |
| Software | SPIDER, package |
| CTF Correction | defocus groups |
| Resolution By Author | 12.8 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 24622 |
| Atomic Model Fitting | |
| Model #0 | |
| Target Criteria | correlation coefficient |
| Details | Protocol: Rigid Body. manual fitting in O |
| Software | O |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| PDB Chain ID | A |
| Fitted Coordinate | |
| PDB entry ID | |
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