A three dimensional model for the 16S rRNA in the ribosome is described that accommodates information for mRNA.16S rRNA interactions as well as accommodating information that has been used as constraints for determining the internal 16S rRNA structure. mRNA.16S rRNA interactions have been summarized from experiments that employ photoaffinity crosslinking to identify sites at which the mRNA comes into close contact with the 16S rRNA. The mRNA track that has been constructed follows a path completely around the middle of the 30S subunit, occupying a space above 16S rRNA domains I and II and below 16S rRNA domain III. The mRNA track contains regions associated with contacts with the 16S rRNA in, and just upstream of, the P tRNA site, associated with contacts around the A site and associated with neighborhoods upstream of the Shine-Dalgarno region and downstream of the decoding region. Structural constraints that come from UV-induced RNA-RNA crosslinks, suggest that the mRNA decoding region lies in a groove between three 16S rRNA duplex regions facing the 50S subunit.
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