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Fitting of L11 protein and elongation factor G (domain G' and V) in the cryo-em map of E. coli 70S ribosome bound with EF-G and GMPPCP, a nonhydrolysable GTP analog
ELECTRON MICROSCOPY
NMR Refinement
Method
Details
Software
Molecular Modeling based on crystal structures
Conformational changes occur in protein L11 and EF-G due to the
binding of EF-G to the 70S ribosome. 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 structures
of L11 and EF-G into the 70S E. coli EF-G (GTP 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 and GMPPCP
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 ...
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 (GTP
form) bound ribosome electron microscopy 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. Conformational changes occur in protein L11 and
EF-G due to the binding of EF-G to the 70S ribosome. 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.