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. 2017 Dec;23(12):1860–1873. doi: 10.1261/rna.061457.117

FIGURE 7.

FIGURE 7.

Model of the PRORP–substrate complex. (A) Overall view of the modeled complex. AtPRORP2 (PDB 5diz, blue) is bound to tRNA (PDB 1ehz, orange backbone with green and blue rings). The AtPRORP1 (PDB 4g24, yellow) NYN and PPR domains are aligned to the corresponding residue domains in AtPRORP2. Purple spheres are the Mn2+ ions bound to the AtPRORP1 active site. Close-up view of the PPR domain highlights the positions of residues for which mutation affected binding affinity (greater than threefold), including D105/N38, N136/Q70, Y140/Y74, N175/N108, T180/T113, R210/R145, and R212/R147 in AtPRORP1/AtPRORP2, respectively. (B) Close-up of the AtPRORP2-tRNA complex with a potential steric clash between NYN helix α21 (red) and the 3′ side of the tRNA acceptor stem. (C,D) Close-up of the AtPRORP2– (C) or AtPRORP1–substrate complex (D) showing the NYN active site. The loop for which AtPRORP2–3 have a four-residue insertion is highlighted in red (C). In both structures, the 5′ leader of pre-tRNA would extend forward from the panel, while the 3′ trailer would extend behind the NYN domain.