RNA structure prediction using positive and negative evolutionary information
Fig 4
CaCoFold structures confirmed by known 3D structures (part 1/7).
Structural elements with covariation support introduced by CaCoFold relative to the Rfam annotation and corroborated by 3D structures are annotated in blue. (a) The A-type RNase P RNA CaCoFold structure includes relative to the Rfam structure one more helix (P6) and two significant covariations, named tr_1 and tr_2. Blue arrows show the placement of these three covarying motifs relative to the 3D structure [46]. The display of the crystal structure has been modified to indicate with back shaded boxes five regions with tertiary interactions labeled “1” to “5”[68]. “tr_1” occurs in region “3” between P8 and the hairpin loop of P14, and “tr_2” in region “4” representing the interaction between P8 and the hairpin loop of P18. The display of the CaCoFold structure has been modified by hand to match the standard depiction of the structure. (b) The SAM-I riboswitch CaCoFold structure shows relative to the Rfam structure one more helix forming a pseudoknot, and a A-U pair stacking on helix P1 both confirmed by the SAM-I riboswitch 2.9 Å resolution crystal structure of T. tengcongensis [47]. CaCoFold also identifies additional pairs with covariation support for helices P2a, P3 and P4. (c) The U4 snRNA CaCoFold structure identifies one more internal loop and one more helix than the Rfam structure confirmed by the 3D structure [48]. The new U4 internal loop flanked by covarying Watson-Crick basepairs includes a kink turn (UAG-AG). The non Watson-Crick pairs in a kink turn (A-G, G-A) are generally conserved (> 97% in this alignment) and do not covary.