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Nucleic Acids Research Advance Access originally published online on October 18, 2007
Nucleic Acids Research 2008 36(Database issue):D178-D183; doi:10.1093/nar/gkm855
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Nucleic Acids Research, 2008, Vol. 36, Database issue D178-D183
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

The 3D rRNA modification maps database: with interactive tools for ribosome analysis

Dorota Piekna-Przybylska, Wayne A. Decatur and Maurille J. Fournier*

Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA

*To whom correspondence should be addressed. Tel: +1 413 545 0566; Fax: +1 413 545 3291; E-mail: 4nier{at}biochem.umass.edu

Received August 23, 2007. Revised September 25, 2007. Accepted September 26, 2007.

The 3D rRNA modification maps database is the first general resource of information about the locations of modified nucleotides within the 3D structure of the full ribosome, with mRNA and tRNAs in the A-, P- and E-sites. The database supports analyses for several model organisms, including higher eukaryotes, and enables users to construct 3D maps for other organisms. Data are provided for human and plant (Arabidopsis) ribosomes, and for other representative organisms from eubacteria, archaea and eukarya. Additionally, the database integrates information about positions of modifications within rRNA sequences and secondary structures, as well as links to other databases and resources about modifications and their biosynthesis. Displaying positions of modified nucleotides is fully manageable. Views of each modified nucleotide are controlled by individual buttons and buttons also control the visibility of different ribosomal molecular components. A section called ‘Paint Your Own’ enables the user to create a 3D modification map for rRNA from any organism where sites of modification are known. This section also provides capabilities for visualizing nucleotides of interest in rRNA or tRNA, as well as particular amino acids in ribosomal proteins. The database can be accessed at http://people.biochem.umass.edu/fournierlab/3dmodmap/


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 J. Biol. Chem.Home page
D. Piekna-Przybylska, P. Przybylski, A. Baudin-Baillieu, J.-P. Rousset, and M. J. Fournier
Ribosome Performance Is Enhanced by a Rich Cluster of Pseudouridines in the A-site Finger Region of the Large Subunit
J. Biol. Chem., September 19, 2008; 283(38): 26026 - 26036.
[Abstract] [Full Text] [PDF]


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