Fig. 4.

Residues at positions 12 and 16 in each PUF repeat contribute to the recognition of specific RNA bases. a Side view of the overall structure of the human Pumilio1 PUF domain bound to NRE2-10 RNA (PDB accession code: 1M8Y). Pum1 is presented as cartoon model and RNA nucleotides are shown in stick representation, with carbons in white, nitrogens in blue, and oxygens in red. b, Enlarged view of recognition of RNA bases of NRE2-10 RNA by the PUF repeats. Residues at positions 12 and 16 from each PUF repeat form hydrogen bonds with one RNA base (shown as black dashed lines) and residue at position 13 stack with RNA bases. PUF repeats are colored in green, with residues that define the specific RNA recognition shown as stick models. c Close-up view of the 12th and 16th residues of PUF repeat 3 contacting the base of the A8 nucleotide through hydrogen bonds. Hydrogen bonds with Q939 and C935 are indicated with black dashed lines. A8 stacks between R936 and H972. d Y1123 and H1159 from repeat 8 form stacking interactions with the uracil base (U3). N1122 (white) and Q1126 (blue) form hydrogen bonds with the uracil base. Hydrogen bonds are indicated by black dashed lines