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!
    Yeast modifications in the active site

    Literature citations:
    For references not cited on this page or in presentation, see Decatur and Fournier, 2002 (1) for relevance.

    Coordinate data and Chime script information:


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

    Last modified July 18th, 2002 by Wayne Decatur