Tour of the Ribosome

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 tour is designed for users with at least a general familiarity with translation and the ribosome, such as students who have taken general biology classes. It is suitable for self-paced study or lectures.

For viewing the tour, you will need a computer capable of using the web browser-based, molecular visualization program called Protein Explorer because this web presentation is a specialized version of Protein Explorer. Protein Explorer requires the free browser plugin, MDL CHIME, available in the company's downloads section. Please, CLICK HERE for more details about Protein Explorer and its computer requirements.

For more Chime-based exploration of the ribosome, see my tour that explores the large ribosomal subunit in greater depth using the true atomic resolution structures of Archaeal large ribosomal particles with and without various transition-state analogs. Besides an introductory tour of the large subunit for the general public I have an intensive tour of the large subunit for specialists. These are all indexed on my home page.

Introduction

The ribosome is a large complex made up of two subunits. Each subunit is made of RNA and protein. The large subunit is responsible for the chemistry of peptide bond formation. A peptide bond is found between every amino acid in a protein. When a ribosome is in the process of protein translation, another amino acid is added to the end of a growing polypeptide chain. The amino acid that is to be added to the chain is attached to the end of a transfer RNA. The growing polypeptide chain is bound to the end of a different transfer tRNA. The tranfer RNAs contact the ribosome during translation. The large subunit of the ribosome is about 100 times large than a typical enzyme and sediments at 50S. The identity of the amino acid that is added is controlled by the small subunit of the ribosome. The small subunit of the ribosome guides the interaction between the messenger RNA (mRNA) and anticodon-ends of transfer RNAs. The small subunit therefore controls the reading of the genetic information stored in genes and does it with exquisite fidelity. Despite its name, the small subunit is still rather large consisting of many proteins and an RNA of substantial length.

In May 2001, Noller and coworkers published a paper in the journal Science detailing the structure of the full ribosome (1). The structural data provided is used here to make a small presentation highlighting the features of the ribosome. The ribosomes used in the crystallization were from a thermophilic eubacteria,Thermus thermophilus. 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. Though the quality of the crystals used for the structure determination was such that atoms less than 5.5 angstroms apart could not be distinguished, it is being treated as an 'effectively atomic-resolution structure' at this time. This is because it is possible to place most individual components at the proper location in the ribosome due to the availibility of other higher resolution structures (2,3,4,5,6). Work will continue in the hopes of even better full ribosome structures. Even though the ribosome structure was highly enlightening, it also raised many questions as well. In the coming years, better ribosome structures should contribute significantly to understanding translation.

CLICK HERE to Begin the Tour of the Ribosome

1. Yusupov , M. M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N. , Cate, J. H.,and Noller, H,F. (2001). Crystal structure of the ribosome at 5.5 A resolution. Science 292:883-96. [Author's note: This is the basis of this tour as it provides much of the data. For more information check in this reference or references therein.]
2. Yusupova ,G.Z., Yusupov, M.M., Cate, J.H., Noller, H.F. (2001). The path of messenger RNA through the ribosome. Cell. 2001 Jul 27;106(2):233-41.
3. Ban, N., Nissen, P., Hansen, J., Moore, P. B., and Steitz, T. A. (2000). The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289:905-920.
4. Nissen, P., Hansen, J., Ban, N., Moore, P. B., and Steitz, T. A. (2000). The structural basis of ribosome activity in peptide bond synthesis. Science 289:920-930.
5. Schluenzen, F., Tocilj, A., Zarivach, R., Harms, J., Gluehmann, M., Janell, D., Bashan, A., Bartels, H., Agmon, I., Franceschi, F., Yonath, A. (2000). Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Cell 102: 615-623.
6. Wimberly, B. T., Brodersen, D.E., Clemons, W. M., Morgan-Warren, R. J., Carter, A. P., Vonrhein, C., Hartsch, T., and Ramakrishnan, V. (2000). Structure of the 30S ribosomal subunit. Nature 407: 327 - 339.
7. Carter, A. P, Clemons, W.M., Brodersen, D.E., Morgan-Warren, R. J., Wimberly, B. T., and Ramakrishnan, V. (2000). Functional insights from the structure of the 30S ribosomal subunit and its interaction with antibiotics. Nature 407: 340-348.

Coordinate data:

• The atomic coordinate data used in this tour is available at the Protein Data Bank.
• The accession numbers of the coordinates related to the ribosome are 1GIX , 1GIY, and 1jgo. (1,2).
• The particular files used here are modified versions of 1GIX and 1GIY and 1jgo.

Acknowledgements:

• This presentation temlate was developed Eric Martz for use in his class Macromolecular Visualization Laboratory. He hopes to soon make it publicly available. Development of the template used to construct this presentation was supported by a grant from the Division of Undergraduate Education of the National Science Foundation. When released, the template will be available as part of the Protein Explorer.
• The original impetus for designing chime-based images of the ribosome was to accompany a series of presentations given in the Fall 2000 Molecular Biology Journal Club at the University of Massachusetts at Amherst. The journal club was run by Professor Maurille 'Skip' Fournier. Positive feedback on those first ones encouraged me to incorporate other structures such as the complete ribosome at 5.5 angstroms used here, as they became available.
• The complex nature of the data used here made it impossible to strictly adhere to the DRuMS color scheme proposed by Tim Driscoll, Freida Reichsman, and Eric Martz, but much of that scheme was used in some manner.

If you like this presentation, please let the author know!

Last updated 1-13-04.