Figure 6.

r(UUCG) structural details derived from X-ray and cryo-EM. (a) A tSW U_2144:B•G_2147:B pair that is part of an r(UUCG) tetraloop showing a water molecule bridging an amino and an imino Watson-Crick site (PDBid: 3U4M). (b,c) Views of the interaction are shown in Figure 1d for two tetraloops extracted from the 7K00 cryo-EM structure. In (c), the density is poor at a 3.0 sigma level and the C422:A residue has been modelled in syn leading to a loss of an important interaction shown in (b) where the density at a higher 5.0 sigma level is unambiguous. Note that X-ray and cryo-EM density sigma levels are not equivalent. (d) Backbone superimposition of the five high-quality 5Y85, 3U4M, 7KKV, 4ARC, and 7K00 r(U_1692:aUCG) Z-turns mentioned in the text. The superimposition was made by using Chimera [73]. (e) View of the 7K00 r(U_420:AUCG) tetraloop with the cytosine in syn and an unrealistic 2.28 Å hydrogen-bond contact [66]. This short contact reveals major modelling issues in regions of a 1.98 Å resolution cryo-EM structure and explains why this tetraloop structure must be discarded.