Three-dimensional visualization of the sites of rRNA modification in the ribosome. The region featured is the multifunctional intersubunit bridge formed by helix 69, which contains a cluster of five modifications created by snoRNPs. (A) Helix 69 depicted in different perspectives of the large subunit and complete ribosome. A panel at the left contains buttons for selecting “pseudouridines” (red), “2′-O-methylations” (green), and “base methylations” (orange). The molecular view on the right includes the large subunit in the 5.5-Å structure with nucleotides equivalent to those modified in yeast helix 69 highlighted; proteins, tRNAs, mRNA, and the small subunit are hidden. The smaller offsets in panel A present the same perspective as in the main view window, but with components made visible sequentially using the convenience control buttons: tRNAs (bottom left), rRNA of the small subunit and mRNA (bottom middle), and proteins of the small and large subunit (bottom right). (B) Helix 69 in a higher resolution structure (2.8 Å); using the “2.8 Å 70S” tool. The panels show the absence (left) and presence (right) of highlighted nucleotides equivalent to those modified in yeast.

Properties of the yeast snoRNA database. The menu bar (top) shows the sections of the database, and portions of the associated links are illustrated in exploded views. “Find snoRNA” and “Target RNA” facilitate searching by different parameters, such as: “name,” “type of snoRNA,” “target RNA,” or “nucleotide targeted.” A representative portion of the main page for an individual snoRNA is shown (below the main menu). Each such page provides basic information about “the snoRNA,” “the DNA coding unit,” “base pairing with the target RNA,” and “corresponding snoRNAs in other organisms.” The positions of the modified nucleotides in rRNA can be visualized in “linear,” “secondary structure,” and “3D structure” formats, with nearby modified nucleotides viewable in linear and secondary structure formats (middle right). Several links are provided to external sites such as Plant and Human snoRNA databases and the Saccharomyces cerevisiae Genome Database (SGD), as exemplified by the SGD ORF map link shown (lower right).