Fig. 4 | Nature Communications

Fig. 4

From: Architecture of the U6 snRNP reveals specific recognition of 3′-end processed U6 snRNA

Fig. 4

3′ end recognition of mature U6 RNA by Lsm2–8 in S. cerevisiae. Comparison of unprocessed U6 and 3′ phosphorylated U6 binding mechanisms. Annealed omit maps (mFo-DFc, 2.5 r.m.s.d.) showing electron density for the phosphorylated U6 ends observed in U6 snRNPs. Lsm5 and Lsm6 are omitted for clarity in panels ac. a In U6 snRNPs with four terminal uridines and a terminal 2′-phosphate, the last nucleotide occupies a 2′- or 3′-uridylate phosphate (Up) binding pocket in the center of the Lsm2-8 ring. b A five-uridine 3′ tail with a terminal 3′-phosphate shifts the binding register to accommodate the terminal nucleotide in the Up pocket. c A previously reported structure of Lsm2–8 bound to a short oligonucleotide with a four-uridine 3’-tail and 2′,3′-cis diol37 has the same register as the five-uridine 3′ tail with a terminal 3′-phosphate, leaving the Up pocket empty. d Detailed view of the Up pocket in the central cavity of Lsm2-8. The terminal 3′-uridylate contacts Lsm2-K20, Lsm3-R21, and the C-terminus of Lsm8. The Lsm3-R21 distance from the terminal phosphate is beyond that for hydrogen bonding, and likely forms a long-range electrostatic interaction, which could be enhanced by the helical dipole in the C-terminal region of Lsm8. e Schematic of U6 3′-end binding by the Lsm2–8 ring. With the exception of Lsm5 and Lsm7, all Lsm proteins harbor canonical Sm-like binding motifs involving planar, cationic, and asparagine residues. Homologous Sm proteins are in parentheses. Residue numbering corresponds to S. cerevisiae. Equivalent residues in the putative nucleotide binding pocket of Lsm1, which replaces Lsm8 in the Lsm1–7 ring, are shown beside the cartoon

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