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. Author manuscript; available in PMC: 2022 Mar 1.
Published in final edited form as: Wiley Interdiscip Rev RNA. 2020 Aug 1;12(2):e1620. doi: 10.1002/wrna.1620

Figure 3. Structure of Danio rerio TRIM71 NHL domain bound to RNA.

Figure 3.

A. The positively-charged cavity on the top surface of Dr Trim71 NHL domain (PDB: 6FPT) (Loedige et al., 2015) was visualized with APBS in PyMOL. Blue denotes positive charge, red denotes negative charge.

B. X-ray crystal structure of the Dr Trim71 NHL domain in complex with the RNA-binding site from the 3’UTR of the mab-10 mRNA (PDB: 6FQL) (Kumari et al., 2018). The RNA stem loop binding site sits within an indentation on the Trim71 NHL domain. Nucleotides that are important for RNA-binding specificity are highlighted in color.

C. The LIN-41 consensus binding motif consists of a short stem with a three nucleotide loop. Specific nucleotides in the loop (position III) and stem (positions −1 &+1) are preferred by LIN-41 and TRIM71 orthologs.