An Interactive Presentation: The 3-D arrangement of modified nucleotides in 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 interactive presentation is designed to accompany a paper entitled rRNA modifications and ribosome function by Wayne A. Decatur and Maurille J. Fournier which is published in the Opinion section of the July 2002 issue of Trends in Biochemical Sciences (1).  

For viewing the presentation, you will need to use Netscape Communicator (Navigator) 4.08 - 4.X since unfortunately Internet Explorer will not (presently but probably soon)work with Protein Explorer, which is the web-based software in which this presentation 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 mini-presentation that should run with most browsers with which the Chime plug-in works.   See the next bulleted line for information on the Chime plug-in.

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 the presentation uses large coordinate data files.   Reducing the size of the files would reduce the user's ability to explore.   I don't recommend trying it at home on a 56K modem.

If you are unfamiliar with the subunit structures, I have put together an introductory tour of the large subunit as well as one for specialists.   Of course, the original papers are also helpful.

Introduction

The ribosome is a large ribonucleoprotein complex made up of two subunits. Atomic-resolution structures of both subunits were first solved in 2000 and subsequent variants have followed (2-12). This advance places the study of the ribosome in new territory. Here, we present 3-D modification maps for E. coli and S. cerevisiae using the structures. By highlighting corresponding nucleotides in the crystal structures, the maps represent visually the approximate spatial arrangement of the modified nucleotides found in ribosomal subunits of E. coli and the S. cerevisiae cytoplasm.

Start the presentation!

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Coordinate data and Chime script information:

• The atomic coordinate data used in this tour was available at the Protein Data Bank.
• The accession codes of the coordinates related to the subunits are 1FFK, 1FFZ,1J5E, and 1LNR (2,3,5,8). The accession codes of the coordinates related to the 70S ribosome are 1GIY and 1JGO (11,12). Consult the Protein Data Bank for the all these coordinate files and information.
• Specifically, modified and combined versions 1FFK and 1FFZ are used in this presentation in order to show the transition-state analog bound in the context of the entire large subunit. In views of the large subunit, domain V in the unbound state is hidden. (Chain :0 is the unbound 23S rRNA and chain :a is the domain V of the bound 23S rRNA.) Even though the scripts state they are loading 1FJF, they actually load the 1J5E file which now supercedes 1FJF.
• The backbone alpha carbons is the extent of the data concerning the proteins of the large subunit in the PDB file used here, but the data is not available with the analog bound in the pdb entry 1JJ2 (50).
• In order to facilitate exploration, the three classes of modifications we consider are assigned terms in the Chime script: A) 'pseudo' refers to pseudouridine and modified-pseudouridine nucleotides; B)'rmethyls' refers to the ribose methyl nucleotides and modified ribose methyl nucleotides, and; C) 'mod' refers to all other modifications in the E. coli scripts, of which all but one in E. coli are methylated base nucleotides. 'basemethyls' is used in the S. cervisiae scripts for all the other modifcations since they are all base-methylated. Users familar with Protein Explorer's Command-line interface can use these terms to refer to the respective group of modified nucleotides.

Acknowledgements:

• Research support for the Fournier lab is from the National Institutes of Health (GM19351).
• This presentation was developed with the technical guidance of Eric Martz in his class Macromolecular Visualization Laboratory.
• 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.

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