Overview of structure of Prp43p bound to an ATP analog and single-stranded RNA. (A) Schematic of S. cerevisiae Prp43p and its structure bound to ADPNP and a single-stranded poly(U) RNA. The schematic (top) illustrates positions of domains and conserved motifs. The structure (bottom) is shown in two orientations. The NTD is colored dark blue; RecA1, green; RecA2, magenta; the 5′HP, yellow; the WH domain, orange; the ratchet domain, teal; the CTD, red; the OB-like fold, brown; the RNA, gray; and ADPNP, multiple colors according to atoms. (B) A 2mFo–DFc electron density omit map surrounding the RNA in complex B is shown, nonaveraged and contoured at 0.8 σ. For clarity, only the RecA1 and RecA2 domains are shown; the RNA is colored according to atom type. (C) Surface representation of the 5′HP and 3′HP, shown bookending the stack of four, intervening bases colored red. (D) Schematic representation of the domain rearrangements in the ADPNP-RNA structure of Prp43p, relative to the ADP structure (PDB 3KX2). The RecA domains are represented as cylinders, with the end of RecA1 colored green and RecA2, magenta; the auxiliary domain is represented as a box, and the RNA, as a black line. Both the rotation of RecA2 and the tilting of the auxiliary domain is indicated. (E) Comparison of the structures of Prp43p in the ADP-bound (gray) and the ADPNP–RNA-bound (colored) states, with the RecA1 domains (green) superimposed. Straight arrows indicate the tilt of the auxiliary domain; the curved arrow shows the rotation of RecA2 around the indicated axis. The location of reference residues, L472 (defining pivot point of the tilt) and T300/P723 (defining axis of rotation), are indicated.
