Role of helical constraints of the EBS1–IBS1 duplex of a group II intron on demarcation of the 5′ splice site

Structure of the ID3 stem–loop showing the 5′ end of the ID3 loop on the left side; the figure on the right is rotated by 180°. The stem of ID3 adopts an A-type helix. Stacking involving bases A7, U8, U9, and A17 continues into the loop, but the riboses of these residues display C2′-endo and mixed conformations. The residues of the EBS1 recognition sequence are not well defined in the family of structures, consistent with a high degree of disorder.