Abridged Tour of the Archaeal Large Ribosomal Subunit

for old Chime versions

by Wayne Decatur,
a research associate in the lab of M. J. Fournier in the department of Biochemistry and Molecular Biology
at the University of Massachusetts, Amherst
.

The abridged tour of the large subunit is designed for a general audience. It is suitable for self-paced study or lectures.

For viewing the abridged tour, you will need to use Netscape Communicator (Navigator) 4.5 - 4.7 since unfortunately Internet Explorer will not work with Protein Explorer, which is the web-based software in which this abridged tour is wrapped. The browser called "Netscape 6" (final release or previews) will not work; "Netscape 6" does not yet support all features found in Netscape's Communicator (Navigator) software. However, there is a Chime-based tour sampler that should run on IE or Netscape 6 running under Microsoft Windows.

The Chime plug-in from MDLI must be installed on your system. Check under "About plug-ins" in Netscape's "Help" menu to see.

Please note that this tour uses large coordinate data files. Every effort has been made to reduce the size and thus the I encourage anyone wishing to explore much more on their own to seek out the original data files as described below.

For a general overview of the full ribosome structure, including both the large and the small subunits, check out my tour of the ribosome.

A more comprehensive tour of the Archaeal Large Ribosomal Subunit exists. In addition to covering the topics seen in the abridged tour, the comprehensive tour provides a more detailed look at many of the features of the subunit, as well as its interactions with two analogs. If you have more than a basic familiarity with the ribosome or have looked at the original set of papers describing the structures (1,2,3), you'd probably better spend your time and learn more by examining the comprehensive tour of the Archaeal Large Ribosomal Subunit. Moreover, the comprehensive tour uses a presentation format designed specifically to deal with the issues raised by the large size of the coordinate data files.

Introduction

The ribosome is a large ribonucleoprotein complex made up of two subunits. The large subunit of the ribosome includes the activity that catalyzes the formation of peptide bonds. The peptidyl transferase reaction is a key step in the cycle of protein synthesis. The cycle includes initiation, elongation, and termination phases and factors that assist, such as elongation factors EF-Tu and EF-G, also bind the large subunit of the ribosome. The large subunit of the ribosome from prokaryotes has a molecular weight of 1.6 million daltons and sediments at 50S. It is made up of two-thirds RNA and one-third protein. The small subunit guides the interaction between messenger RNA (mRNA) and anticodon-ends of transfer RNAs to read the genetic information stored in genes with exquisite fidelity. It sediments at 30S in prokaryotes.

In the summer of 2000, the Steitz and Moore labs published a series of papers in the journal Science detailing the structure of the large subunit of the Archaeal Ribosome at 2.4 angstroms resolution (1,2,3). The structural data provided is used here to make a small presentation of the features of the large ribosomal subunit and highlight some of the implications of this landmark achievement. The subunit was purified from a rather obscure organism, the archaea Haloarcula marismortui. However, due to the high conservation of ribosomal RNA and proteins, the data has immediate value for investigators interested in the machinery that makes proteins in every organism on earth. Additionally, not only did they elucidate a high resolution structure of the large subunit rRNA and most of its associated proteins, but they also soaked in analogs of substrates and solved structures with these bound in the subunit. These additional structures provide crucial clues to the interactions necessary to produce polypeptides from the basic building blocks of amino acids. Not only is this a stunning revelation for the translation field, but this structure represents the first molecular structure on this grand of a scale determined at atomic resolution. In the following months two high resolution structures of a eubacterial small ribosomal subunit were published (4,5,6). The year 2000 stands as a banner year in science. With the (near) completion of human genome and the high resolution structures of the large and small ribosomal subunits, marvelous vistas at both ends of the spectrum of gene expression were first truly glimpsed.

This is just the first atomic resolution structure of the large ribosome subunit. Even though the subunit structure was highly enlightening, it also raised many questions as well. Just as in the years prior to determination of the first atomic resolution subunit structure, the work on the subunit will continue steadily. In the coming years, progressively higher resolution structures of the large subunit from Haloarcula and other organisms, both alone and complexed with the small subunit, should contribute significantly to further elucidating the complexities of translation.