Table 1.

Major differences between the apo- and RNA-bound U2AF⁶⁵ RRM1 structures ^a

Region	apo-U2AF65RRM1	RNA-bound U2AF65RRM1	Figure
β2/β3 loop	Poorly ordered	Well ordered, shifts to interact with RNA	Figure 1(b)
Water molecules near β2/β3 loop	Prepositioned for RNA interactions	Interacts with Uri3 & Uri4	Figure 1(b); Supp. Figure 1
Aromatic residues in RNP motifs	Well ordered	Slight shifts to stack with RNA bases	Figure 2(c)
Arg150	Major conformation interacts with Gly146 & Glu201; Minor conformation stacks with symmetry-related Phe158 and is most frequent rotamer (44%)	Only minor conformation of apo-RRM1-Arg150 is observed, which stacks with RNA base	Figure 2(d)
Lys225	Major conformation is most frequent rotamer (42%); Minor conformation is second most frequent rotamer (25%)	Only minor conformation of apo-RRM1-Lys225 is observed, which interacts with RNA	Figure 2(e)
Arg227	Major conformation interacts with Glu215; Minor conformation is the most frequent rotamer (44%)	Only major conformation of apo-RRM1-Arg227 is observed, which interacts indirectly with RNA via water molecule, and directly with Glu215 & dioxane from cryosolvent; Minor conformation would be too close to RNA-bound Lys225 conformation (3.3Å Nζ-NH1 distance)	Figure 2(e)

^aDescriptions of minor alternative conformations are distinguished by italics.