Figure 3: Structure of the Roquin-1 ROQ domain bound to Ox40 ADE-like RNA.

(a) Cartoon presentation of the crystal structure of the ROQ domain (residues 174–325; blue) and the Ox40 ADE-like SL RNA (magenta). Selected RNA bases and protein secondary structure elements are labelled. (b) Close-up view of the Ox40 ADE-like SL (bases in the RNA hexaloop are shown in magenta) and (c) the previously reported structure of the ROQ-Tnf CDE complex¹¹ (bases of the triloop RNA are shown in green). Only RNA-interacting residues that are different in both structures are shown. Both protein chains and remaining parts of both RNAs are shown in grey and protein residue side chains are shown in turquoise. (d) Close-up view of the contacts between the ROQ domain and nucleotides U11 and U13 of the Ox40 ADE-like SL RNA. The nucleotides interact with the C-terminal end of helix α4 (Tyr250 and Ser253) and the N-terminal part of strand β3 (Phe255 and Val257). The protein chain is shown in turquoise and the RNA is shown in grey. Atoms are colour coded according to charge. (e) Close-up view of the contacts between the ROQ domain and nucleotides U10, U11 and U13 in the RNA hexaloop. U11 and U13 contact the C-terminal end of helix α4: residues Tyr250 and Gln247. The side chain of Tyr250 makes hydrophobic interactions with the pyrimidine side chain of U10 on one side and U11 on the other side. Lys259 interacts with the phosphate groups of U10 and U11. (f) Close-up view of the hydrophobic interaction between Val257 and U11, as well as the double hydrogen bond of Lys259 with phosphate groups of U10 and U11. In d – f, amino acids are shown in turquoise and blue, nucleotides in grey colour. See also Supplementary Notes and Supplementary Fig. 2.