Fig. 1

The cryo-EM structure of the ternary complex. a Schematic diagrams of SpCas9, 98-nt sgRNA, 55-bp target DNA. Potential Watson–Crick and non-Watson–Crick base pairs in sgRNA and DNA are indicated by lines and dots, respectively. b Representative 2D classes of the complex particles. The positions of the PAM proximal and PAM distal ends of the target DNA are indicated by arrows 1 and 2, respectively. c Rigid-body fitting of the crystal structure 4OO8 in the absence of the HNH domain, with a correlation coefficient of ~0.80. The density map at a higher contour level (~4.0σ) shows clearly most of the SpCas9 α-helices in the crystal structure (cartoon model). The central, small panel shows the EM density that resolves the long bridge helix. d The density map clearly resolves sgRNA, the RNA:DNA heteroduplex, PAM, and the PAM proximal end in the crystal structures (4OO8 and 4UN3, cartoon model). The correlation coefficient of the rigid-body fitting of 4UN3 is ~0.80