Role of the central junction in folding topology of the protein-free human U2–U6 snRNA complex

Predictive computational models of the two major conformers of the human U2–U6 snRNA complex obtained by simulation using SimRNA (Magnus et al. 2016), with distance restraints between dyes determined experimentally and visualized by NGLview (Nguyen et al. 2018). (A,B) Models of the four-helix junction conformer (Helix I/III in red; U6 ISL in blue; U2 Stem I folded behind the junction in green; Helix II in violet) (A) without Mg²⁺ and (B) with 40 mM Mg²⁺, showing a compaction of Helix I/III, ISL, and Helix II around the junction (Stem I is folded behind the junction in this view). (C,D) Models of calculated three-helix junction conformer with three helices (Helix I/III in red; U6 ISL in blue; Helix II in gray) (C) without Mg²⁺ and (D) with 40 mM Mg²⁺, showing a widened junction. The position of Helix II in the three-helix conformer was not experimentally determined but found to be in the lowest energy position by simulation.