Atomic resolution models, ribosomal

Atomic Resolution Models for the Ribosomal Decoding Site... 

Many medium resolution structures of macromolecular assemblies (e.g., ribosomes), spherical and helical viruses, and larger protein molecules have now been determined by electron cryomicroscopy in ice. Four atomic resolution structures have been obtained by electron cryomicroscopy of thin 2D crystals embedded in glucose, trehalose, or tannic acid (11-14), where specimen cooling reduced the effect of radiation damage. One of these, the structure of bacteriorhodopsin (1 l)provided the first structure of a seven-helix membrane protein. The medium resolution density distributions can often be interpreted in terms of the chemistry of the structure if a high resolution model of one or more of the component pieces has already been obtained by X-ray, electron microscopy, or NMR methods. As a result, the use of electron microscopy is becoming a powerful technique for which, in some cases, no alternative approach is possible. Useful reviews [e.g., Dubochet et al. (9), Amos et al. (15), Walz and Grigorieff (16), and Baker et al. (17)] and a book [Frank (18)] have been written. 

Macromolecular models should have a level of resolution commensurate with the quality and quantity of available data. We have developed a package of programs for building and refining models of nucleic acids and protein-nucleic acid complexes, with different levels of detail in different parts of the molecule. The method incorporates data from a variety of experiments. Our RNA models have atomic detail in some regions and lower resolution (typically one pseudoatom per nucleotide) in others. We are using this approach to refine models for the 308 subunit of the E. coli ribosome, with emphasis on the decoding site, where the 168 rRNA holds the mRNA and two tRNAs. 

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