Secondary structure and domain architecture of the 23S and 5S rRNAs

We present a de novo re-determination of the secondary (2 degrees) structure and domain architecture of the 23S and 5S rRNAs, using 3D structures, determined by X-ray diffraction, as input. In the traditional 2 degrees structure, the center of the 23S rRNA is an extended single strand, which in 3D is seen to be compact and double helical. Accurately assigning nucleotides to helices compels a revision of the 23S rRNA 2 degrees structure. Unlike the traditional 2 degrees structure, the revised 2 degrees structure of the 23S rRNA shows architectural similarity with the 16S rRNA. The revised 2 degrees structure also reveals a clear relationship with the 3D structure and is generalizable to rRNAs of other species from all three domains of life. The 2 degrees structure revision required us to reconsider the domain architecture. We partitioned the 23S rRNA into domains through analysis of molecular interactions, calculations of 2D folding propensities and compactness. The best domain model for the 23S rRNA contains seven domains, not six as previously ascribed. Domain 0 forms the core of the 23S rRNA, to which the other six domains are rooted. Editable 2 degrees structures mapped with various data are provided ( ext-link-type=uri xlink:href=http://apollo.chemistry.gatech.edu/RibosomeGallery xmlns:xlink=http://www.w3.org/1999/xlink>http://apollo.chemistry.gatech.edu/RibosomeGallery).