RNA structure prediction using positive and negative evolutionary information
Fig 5
CaCoFold structures confirmed by known 3D structures (part 2/7).
Structural elements with covariation support introduced by CaCoFold relative to the Rfam annotation and corroborated by 3D structures are annotated in blue. (a) Relative to the Rfam structure, the Cobalamin riboswitch CaCoFold structure adds one pseudoknot and one Watson-Crick basepair defining a four-way junction between helices P1, P2, and P3, both confirmed by the S. thermophilum crystal structure [49]. It also adds more covariation support for helices P1 and P2. (b) In CaCoFold structures, alternative helices that do not overlap with the nested structure are annotated as pseudoknots (pk), otherwise they are annotated as triplets (tr). For structures obtained from a crystal structure, non Watson-Crick basepairs are annotated as non-canonical (nc) regardless of whether they are overlapping or not with the nested structure. The tRNA CaCoFold structure has been re-annotated manually to match the labeling of the S. cerevisiae phenylalanine tRNA 1EHZ crystal structure (1.93 Å) for all common basepairs [51]. Of the covarying pairs in the CaCoFold structure but not in the Rfam tRNA structure, five (depicted in blue) are confirmed by the 1EHZ structure as analyzed by RNAView. The sequence of the 1EHZ tRNA does not include the V loop, which appears in 16% of the 954 sequences in the Rfam tRNA seed alignment. Two covarying pairs (depicted in orange) appear to be the result of constraints other than RNA structure. The remaining six covarying pairs are labeled in black. Four basepairs identified in the 3D structure but not incorporated in the CaCoFold structure are depicted in brown. The annotation of the non Watson-Crick pairs with at least two H-bonds follows the nomenclature of [34] that reports the two edges of the nucleotides involved in the plain of the H-bonds. “W” stands for the Watson-Crick edge, “S” for the Sugar edge, and “H” for the Hoogsteen face; “c” and “t” stand for cis and trans respectively. WWc is a standard Watson-Crick basepairs. (c) In the U2 spliceosomal RNA, Stem IIa and Stem IIc, both with covariation support, are two alternative helices that compete to promote different splicing steps [53].