Fitting of L11 protein and elongation factor G (EF-G) in the cryo-em map of e. coli 70S ribosome bound with EF-G, GDP and fusidic acid
ELECTRON MICROSCOPY
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Molecular Modeling based on crystal structures | Conformational changes occur in protein L11 and EF-G in two stpes due to the binding of EF-G to the 70S ribosome, and subsequent GTP hydrolysis. These changed conformations were modeled based on the fitting of the crystal coordinates to the low resolution ribosome map (factor-bound) and energy minimizing the fitted structures. | IRIS Explorer |
| Additional NMR Experimental Information | |
|---|---|
| Details | This structure was generated by fitting the X-ray crystal structure of L11 and EF-G into the 70S E. coli EF-G (GDP form) bound ribosome map. L11 (linker region between N and C terminal) and EF-G positions of domains G' and V were modeled to accommodate the conformational changes. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | data analysis | IRIS Explorer | 3.5 | Numerical Algorithms Group, Inc. |
| 2 | data analysis | O | 5.10 | Jones, Zou, Cowan, Kjeldgaard |
| 3 | processing | SPIDER | 4.48 | Frank |
| 4 | data analysis | Insight II | 1998 | Biosym/MSI Inc. |
| Sample |
|---|
| e. coli 70S ribosome bound with EF-G, GDP and fusidic acid |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 36113 |
| Reported Resolution (Å) | 18 |
| Resolution Method | FSC 0.5 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | VISUAL AGREEMENT | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | REFINEMENT PROTOCOL--MANUAL DETAILS--This structure was generated by fitting the X-ray crystal structure of L11 and EF-G into the 70S E. coli EF-G (G ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GENERIC FILM | ||||||||
| Electron Dose (electrons/Å**2) | 10 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI/PHILIPS EM420 |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | GATAN LIQUID NITROGEN |
| Nominal Magnification | 52000 |
| Calibrated Magnification | |
| Source | OTHER |
| Acceleration Voltage (kV) | |
| Imaging Details |
