1JQM
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 | ||
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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 | |
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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 | ||||
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# | 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 |
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e. coli 70S ribosome bound with EF-G, GDP and fusidic acid |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
3D Reconstruction | |
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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 | |||||
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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 | |||||||||
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Detector Type | GENERIC FILM | ||||||||
Electron Dose (electrons/Å**2) | 10 |
Imaging Experiment | 1 |
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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 |