title: Secondary structures of rRNAs from all three domains of life.
abstract: Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rRNAs. We identify helices by specific geometric and molecular interaction criteria, not by co-variation. The structural approach allows us to incorporate non-canonical base pairs on parity with Watson-Crick base pairs. The resulting rRNA 2° structures are up-to-date and consistent with three-dimensional structures, and are information-rich. These 2° structures are relatively simple to understand and are amenable to reproduction and modification by end-users. The 2° structures made available here broadly sample the phylogenetic tree and are mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution. We have generated 2° structures for both large subunit (LSU) 23S/28S and small subunit (SSU) 16S/18S rRNAs of Escherichia coli, Thermus thermophilus, Haloarcula marismortui (LSU rRNA only), Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We provide high-resolution editable versions of the 2° structures in several file formats. For the SSU rRNA, the 2° structures use an intuitive representation of the central pseudoknot where base triples are presented as pairs of base pairs. Both LSU and SSU secondary maps are available (http://apollo.chemistry.gatech.edu/RibosomeGallery). Mapping of data onto 2° structures was performed on the RiboVision server (http://apollo.chemistry.gatech.edu/RiboVision).
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America.
authors: Anton S
authors: AS
authors: Petrov
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America.
authors: Chad R
authors: CR
authors: Bernier
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America.
authors: Burak
authors: B
authors: Gulen
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America.
authors: Chris C
authors: CC
authors: Waterbury
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America.
authors: Eli
authors: E
authors: Hershkovits
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America.
authors: Chiaolong
authors: C
authors: Hsiao
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America.
authors: Stephen C
authors: SC
authors: Harvey
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America.
authors: Nicholas V
authors: NV
authors: Hud
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America.
authors: George E
authors: GE
authors: Fox
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America.
authors: Roger M
authors: RM
authors: Wartell
authors: Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America.
authors: Loren Dean
authors: LD
authors: Williams
mesh_terms: D000818:Animals; D020029:Base Pairing; D004331:Drosophila melanogaster / Q000737:chemistry / Q000235:genetics; D019614:Haloarcula marismortui / Q000737:chemistry / Q000235:genetics; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D019642:RNA, Archaeal / Q000737:chemistry / Q000235:genetics; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012331:RNA, Fungal / Q000737:chemistry / Q000235:genetics; D012335:RNA, Ribosomal / Q000737:chemistry* / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics; D016963:Thermus thermophilus / Q000737:chemistry / Q000235:genetics
chemical_list: D019642:RNA, Archaeal; D012329:RNA, Bacterial; D012331:RNA, Fungal; D012335:RNA, Ribosomal