Movie S2.

Structural changes of HIV-1 RT from the RNase H inactive (PDB ID code 4B3O) (2) to active form (crystal 1; PDB ID code 6BSH). The two structures were first superimposed using p51 subunits. P51 is shown in silver, and p66 is shown in multiple colors: pink, palm; steel-blue, fingers; pale-green, thumb; light-aqua, RNase H; and yellow-orange, connection domain. The RNA and DNA strands are shown in red and blue, respectively. The RNase H active site residues D443, E478, D498, and D549 are shown as red sticks, and two Ca2+ ions in the RNase H active site are shown as green spheres. The parts of RT undergoing conformational changes are highlighted as follow: magenta for the three loops in the CN and RNase H domains of p66 that allow the contraction between the thumb and RNase H, forest green for the p51-p66 interface that binds the RNA strand, and orange for the helices that are repacked between p51 and p66 interface.