Conformational transition of Cas9:precat (5F9R.pdb) into Cas9:DNA (4UN3.pdb). The X-ray structure of Cas9:precat is slowly dragged into the X-ray structure of Cas9:DNA upon removal of the nontarget DNA (nt-DNA) strand. A TMD approach is used. Cas9 is shown as cartoons, with individual protein domains color-coded as in Fig. 1. The RNA (orange) and target DNA (t-DNA) strands are shown as ribbons.