Tour of the Archaeal Large Ribosomal Subunit for Specialists

• The tour of the Archaeal Large Ribosomal Subunit is a user-controlled, web browser-based presentation suitable for self-paced study or for lectures.
• The tour of the Archaeal Large Ribosomal Subunit is for specialists.   I have made a tour for the general public that is abrdiged to simply touch upon many of the highlights. It uses Eric Martz's facile Protein Explorer Interface.
• For viewing the full tour, you will need to use Netscape Communicator (Navigator) 4.5-4.7   (NOT Netscape 6!).   However, for users of Netscape 6 or Internet Explorer under Microsoft Windows OS, there is a Chime-based tour sampler that runs in those browsers.)
• The Chime plug-in (version 2.0 or better) from MDLI must be installed on your system. See Chime Resources at UMASS for more information. You can check if Chemscape Chime plug-in is installed in Netscape Communicator (Navigator) by looking in the "About Plug-ins" option under the "Help" menu.   Chime is fast becoming the standard for molecular visualization and worth the short download.
• 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.   If you find the download times impeding your enjoyment, I have made downloadable versions of the full tour available for both PC and Mac.   However, they may not always be as current as the online version.
  A Brief Introduction to the Large Subunit Structure 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 2.6 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 an interactive tour to detail 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.

  Begin the Tour of the Archaeal Large Ribosomal Subunit
  

1. Cech, T.R.. (2000). The ribosome is a ribozyme. Science. 289: 878-879.
2. 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. [Author's note: This and the next reference are a basis of this tour as they provide much of the data. Therefore, if a detail lacks a specific reference, for more information check in this reference, reference #3, or references therein.]
3. 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.
4. 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.
5. 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.
6. 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.
7. Hanna, R. and Doudna, J.A. (2000). Metal ions in ribozyme folding and catalysis. Curr. Opin. Chem. Biol. 4:166-70.
8. Trakhanov, S. and Quiocho, F.A. (1995). Influence of divalent cations in protein crystallization. Protein Sci. 4:1914-1919.
9. Wool, I. G., Gluck, A., Endo, Y. (1992). Ribotoxin recognition of ribosomal RNA and a proposal for the mechanism of translocation. Trends Biochem. Sci. 17: 266-269.
10. Samaha, R. R., Green, R., and Noller, H. F. (1995). A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome. Nature 377: 309-314.
11. Green, R., Switzer, C., and Noller, H. F. (1998). Ribosome-catalyzed peptide-bond formation with an A-site substrate covalently linked to 23S ribosomal RNA. Science 280: 286-289.
12. Puglisi EV, Green R., Noller H.F., and Puglisi J.D. (1997). Structure of a conserved RNA component of the peptidyl transferase centre. Nat. Struct. Biol. 4:775-778.
13. Khaitovich, P., Mankin, A.S., Green, R., Lancaster, L., and Noller, H.F. (1999). Characterization of functionally active subribosomal particles from Thermus aquaticus. Proc. Natl. Acad. Sci. U. S. A. 96: 85-90.
14. Muth, G. W., Ortoleva-Donnelly, L., and Strobel, S.A. (2000). A single adenosine with a neutral pKa in the ribosomal peptidyl transferase center. Science 289:947-950.
15. Weinstein, L.B. and Steitz. J.A. (1999). Guided tours: from precursor snoRNA to functional snoRNP. Curr. Opin. Cell Biol. 11:378-384.
16. Sirum-Connolly, K. and Mason, T.L. (1995). Functional requirement of a site-specific ribose methylation in ribosomal RNA. Science 262:1886-1889.
17. Wower, J., Kirillov, S.V., Wower, I.K., Guven, S., Hixson, S.S., Zimmermann, R.A. (2000). Transit of tRNA through the Escherichia coli Ribosome. Cross-linking of the 3' end of tRNA to specific nucleotides of the 23 S ribosomal RNA at the A, P, and E sites. J. Biol. Chem 275: 37887-37894.

Coordinate data:

• The atomic coordinate data used in this tour was available at the Protein Data Bank.
• The accession numbers of the coordinates related to the subunit are 1FFK, 1FFZ, and 1FG0 (2,3).
• The accession number of the NMR data of a small RNA with the sequence of a conserved part of the ribosomal RNA of the large subunit is 1VOP (12).

Acknowledgements:

• This tour was developed from a collection of Chime-images initially produced by Wayne Decatur 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 and the presentations included talks by members of the labs of Thomas Mason, Robert Zimmermann, and Maurille Fournier.
• Numerous people aided in its design. Bruce Maguire, Thomas King, Ben Liu, Joseph Bengiovanni, Skip Fournier, and Thomas Mason assisted in topic selection and provided help with scientific concerns.
• Technical advice and guidance were provided by Eric Martz and Freida Reichsman with some initial pointers from Kelcy Newell.
• For the most part, I have utilized the DRuMS color scheme proposed by Tim Driscoll, Freida Reichsman, and Eric Martz.
• Most of the scripts for the images in this presentation were designed and debugged in professor Eric Martz's easy-to-use Protein Explorer. He also developed a template for presentations in Chime which was used as a starting point for developing this tour. That template has been made somewhat outdated by development of his new presentation template, which 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. However, the old template actually seemed a better starting point for developing the comprehensive tour of the large ribosomal subunit as the large coordinate files and complex scripts dictated a simplified style and inlcusion of some special features which were more easily designed into the older, basic template.

• October 20 - November 20,2000, version 1.00Beta development.
• December, 5th posted downloadable versions of 1.00Beta.
• December, 6th 2000 fixed some parts of text - version 1.01Beta.

For computers running Microsoft windows:
Click subunit.exe and save to disk.
While you wait you can make a new folder into which you can unpack the files.   After downloading subunit.exe, double-clicking on the downlaoded file should initiate unzipping.   Unzip it into the new folder you made.   When unpacked, you want to open the file named "index.htm" with Netcape Communicator (Navigator) to take the full tour.


For Macs:
Click subunit.sit.bin and save to disk.
After downloading drag to Stuffit Expander on your computer and it should unpack. Stuffit Expander is a freeware program available for download from Aladdin Systems.  It should automatically unpack into one folder named "ribosome".   When unpacked, you want to open the file named "index.htm" with Netcape Communicator (Navigator) to take the full tour.

This and other Chime-based tutorials are indexed at the World Index of Molecular Visualization Resources (linked to the UMass Chime Resources Site). This particular one is under the category Biochemistry Tutorials in Chime.

If you like this presentation, please let the author know! Or if you would like to download a copy of this presentation to facilitate classroom use or to enable easier use, please contact Wayne Decatur.

Start the Tour of the Archaeal Large Ribosomal Subunit