Fig. 1
From: Structural and biochemical insights into small RNA 3′ end trimming by Arabidopsis SDN1
Structure of SDN1 ΔC-ssRNA complex. a Domain architectures of Arabidopsis SDN1 and SDN2. NTD, N-terminal domain; DEDDh, the catalytic domain; RRM, the C-terminal domain found to adopt an RRM fold in this study. The numbers of amino acid residues are as indicated. b Front and side views of SDN1 bound to the single-stranded RNA in cartoon mode. Domains are colored as in a. c The surface electrostatic potential of SDN1 ΔC showing that the 3′ end of the RNA is inserted into the negatively charged catalytic pocket. Red, −5.0 kBT/e; Blue, + 5.0 kBT/e. kB, Boltzmann constant; T, temperature in Kalvin; e, charge of an electron. d The molecular surface of SDN1 ΔC showing the extensive interface between the NTD and the DEDDh domain. The structure also shows that the interaction of SDN1 with the RNA occurs mainly through the DEDDh domain. e–g Hydrophobic interactions and hydrogen bond networks between the NTD and DEDDh domains. Glu96, Thr103, Asp121, Phe123, and Ser125 in NTD form hydrogen bonds with Arg165, Gln207, Lys233, Asp235, His236, and Asp241 in the DEDDh domain (H-bonds shown in red dotted lines). The various hydrophobic interactions are depicted in e to g. e Phe123 interacts with Ile234 and Leu214, and the side chain of Lys233 packs against the aromatic ring of Trp122. f Leu99, Val100 and Leu102 on helix α5 of the NTD are buried in the hydrophobic surface formed by Ile240, Val245 and Val294 in the DEDDh domain. g the aromatic rings of Tyr109, Tyr113, and Phe115 protrude into the hydrophobic surface formed by Leu225, Leu229, Val239, and Leu244 in the DEDDh domain
