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.
Please note that this tour uses huge coordinate data files; at the time the subunit data file was deposited, the single file actually contained about 5 times more RNA structural data than previously in the entire structural database. Thus, the tour will not work well over a 56K modem.
The ribosome is a large ribonucleoprotein complex made up of two subunits. The small subunit of the ribosome includes the activity that decodes the genetic message.
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 and is about 1 million daltons!
In the fall of 2000, both the Ramakrishnan lab and the Yonath lab published a series of papers (1,2,3).
Not only did they elucidate a high resolution structure of the small subunit rRNA and most of its associated proteins, but they also went on to soak in analogs of substrates and solve structures with these bound in the subunit (4,5).
These structures provide crucial clues to the interactions necessary to decode the genetic message in the course of protein synthesis by the ribosome.
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 1fjf and 1ibm (1,5).
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 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.
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