A database of maps showing the sites of modified
rRNA nucleotides in three-dimensional models

The menu bar above provides access to the rRNA seqeunces wtih modifications sites indicated, secondary structures with modifications sites indicated, 3D modifiction maps and the supporting tables of equivalent nucleotides for rRNA from model organisms.

This database complements the Yeast snoRNA Database at UMass-Amherst and relies on linking to some content from that database, as well as to others by colleagues in related fields. Therefore, please be very cognizant as to the source when citing information obtained herein.

If you make use of the data presented here, please cite the following article in addition to the primary data sources:
- D. Piekna-Przybylska, W. A. Decatur, and M. J. Fournier (2007). The 3D rRNA modification maps database: with interactive tools for ribosome analysis. Nucleic Acids Research.Jan;36:D178-83. Epub 2007 Oct 18.


What's new

August 2007:
A fully operational version of this database is now publically available.

September 2007:
A tRNA Nucleotide selector interface has been added to the panel of convenience buttons as an option for all the 3D visualizations using the 5.5 Å ribosome structure and for some using the 2.8 Å ribosome structure.
A means to change the thickness of the rRNA and proteins ribbons/backobne has been added to the panel of convenience buttons as an option for all the 3D visualizations using the 5.5 Å and 2.8 Å ribosome structures.

October 2007:
The manuscript describing this database is now viewable at the Nucleic Acids Research website. Click here to access it.

March 2009:
Versions of 3D modification maps for yeast and E. coli were added where the parts of the A-site tRNA (nts 1-25 and 45-76) not visible in the 2.8 Å structure were added back for a complete A-site tRNA. This was done by modeling the 5.5 Å structure (1gix/1jgo) tRNAs onto the tRNAs in the 2.8 Å structure and removing all the 5.5 Å structure tRNA atoms except for those not visible in the 2.8 Å structure. Such a model was also added as a choice for the 'Paint Your Own' section. These three new versions include tRNA Nucleotide selector interface on the panel of convenience buttons as well.

Last update: March 23, 2009 5:08 PM.
© 2009 University of Massachusetts Amherst. Site Policies.
This site is maintained by Wayne Decatur of the Fournier Lab in
the Department of Biochemistry and Molecular Biology

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