The cross-link from the upstream region of mRNA to ribosomal protein S7 is located in the C-terminal peptide: Experimental verification of a prediction from modeling studies

The recent rapid advances that have been made both in cryo-electron microscopy (cryo-EM) and X-ray crystallography of bacterial ribosomes or their subunits (e.g., Stark et al., 1997a, 1997b; Ban et al., 1998; Malhotra et al., 1998) have led to a correspondingly rapid advance in our understanding of the three-dimensional (3D) arrangement in situ of the ribosomal RNA and protein molecules. In 1997 we published a model for the 16S rRNA (Mueller & Brimacombe, 1997a), which was fitted to a cryo-EM reconstruction at 20 Å resolution of the Escherichia coli 70S ribosome carrying tRNAs at the ribosomal A and P sites (Stark et al., 1997a). Subsequently, on the basis of the available RNA–protein interaction data (Mueller & Brimacombe, 1997b), we were able to fit the structure of ribosomal protein S7 as determined by X-ray crystallography (Hosaka et al., 1997; Wimberly et al., 1997) into our model in such a way as to satisfy both the biochemical data and the electron density of the EM reconstruction (Tanaka et al., 1998). More recently, the 16S model has been refined to fit an EM reconstruction at 13 Å resolution (Brimacombe et al., 2000), the latter being itself a refinement of the published EM reconstruction at 18 Å (Stark et al., 1997b) of 70S ribosomes carrying an EF-Tu/tRNA ternary complex stalled with the antibiotic kirromycin. In the refined 16S model, only minor changes needed to be made in the arrangement of the rRNA region interacting with S7 and in the positioning of the protein itself.