5S Ribosomal RNA Database

Abstract

Ribosomal 5S RNA (5S rRNA) is an integral component of the large ribosomal subunit in all known organisms with the exception only of mitochondrial ribosomes of fungi and animals. It is thought to enhance protein synthesis by stabilization of a ribosome structure. This paper presents the updated database of 5S rRNA and their genes (5S rDNA). Its short characteristics are presented in the Introduction. The database contains 2280 primary structures of 5S rRNA and 5S rRNA genes. These include 536 eubacterial, 61 archaebacterial, 1611 eukaryotic and 72 organelle sequences. The database is available on line through the World Wide Web at http://biobases.ibch.poznan.pl/5SData/.

Figure 1

The general secondary structures of 5S ribosomal RNA of Eukaryota (A) and Eubacteria (B). The numbering of the nucleotides corresponds to that in the multiple sequence alignments available from the database web pages. The positions of rare insertions are shown as black squares. The nucleotide symbols used in diagrams are according to IUBMB nomenclature. N: A, C, G or U; Y: C or U; R: A or G; W: A or U; S: G or C; M: A or C; K: G or U.

Figure 2

The secondary structure and tertiary interactions of H.marismortui 5S rRNA as observed in the crystal structure of large ribosomal subunit. Watson–Crick and wobble base pairs are shown as thick lines, non-canonical base pairs are shown as open circles. Nucleotides involved in the tertiary interactions (thin lines) are shown as black circles.