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. Author manuscript; available in PMC: 2020 Jan 8.
Published in final edited form as: Nat Struct Mol Biol. 2019 Jul 8;26(8):679–685. doi: 10.1038/s41594-019-0258-2

Fig. 3. HNH domain adopts catalytic conformation in state II.

Fig. 3.

(a) A conformational change of the HNH domain during transition from state I to state II. The HNH domain in state I (beige cartoon) rotates around a central axis (grey rod) and translates ~34 Å to reach the scissile bond in TS (shown with dashed circle, and either arrow or asterisk) where it adopts an active conformation (pink cartoon). The nucleic acid backbone is colored as in Fig. 1 with the rest of Cas9 shown in grey transparent surface. (b) Close-up view of the catalytically-competent active site of HNH in state II with ball-and-stick representation of the catalytic site. The newly formed 5’- and 3’-ends of the cleaved TS are shown in blue, with hydrogen bonds shown as dashed lines. (c) Cryo-EM density maps and models spanning the cleavage site demonstrate that the TS is intact in state I and cleaved in states II and III. Arrow designates the scissile bond in state I, while the asterisk marks the cleaved phosphodiester bond in states II and III.