Three dimensional model for the 16S ribosomal RNA in the Escherichia coli ribosome

Molecular modeling has been performed to help correct and refine an approximate three dimensional structure for Eschericia coli 16S rRNA that originated as hand-built wire model. The wire model was built to accommodate the base pairs in 16S rRNA (1), mRNA.16S rRNA interactions (2,3), rRNA.ribosomal protein interactions (see 4), ribosomal protein-ribosomal protein distances (5), intramolecular RNA-RNA UV-crosslinks (6,7) and site-directed mutagenesis experiments (8). In the computer model, individual base-paired regions were constructed separately and then were installed into the expected locations to produce the entire structure. We describe here the considerations, steps and results of this refinement process.