Fig. 3

Structural analysis of activated Cas12a RNPs with divalent cations on the basis of AlphaFold3. A Structural comparison between the simulation model based on AlphaFold3 using the activated Cas12a RNP (purple) and the activated Cas12a RNP with Mg²⁺ (red) (RMSD = 0.064). B Molecular simulation estimates of distance changes between Val377 and Gln1136 due to the Cas12a conformation changes resulting from Mg²⁺ by AlphaFold3. The Val377–Gln1136 distance in activated Cas12a RNPs with Mg²⁺ is 32.80 Å, which is similar to the 32.55 Å distance in activated Cas12a RNPs. Green: Cas12a protein; blue: nuclease domain (NUC) in Cas12a; parakeet: gRNA; magenta: ssDNA trigger; pink: Mg²⁺. C Structural comparison between the simulation model based on AlphaFold3 using the actual activated Cas12a RNP (purple) and activated Cas12a RNP with Mn²⁺ (yellow) (RMSD = 0.063). D Molecular simulation estimates of distance changes between Val377 and Gln1136 due to the Cas12a conformation changes resulting from Mn²⁺ by AlphaFold3. The Val377–Gln1136 distance in activated Cas12a RNPs with Mn²⁺ is 32.69 Å, which is similar to the 32.55 Å distance in activated Cas12a RNPs. Green: Cas12a protein; blue: nuclease domain (NUC) in Cas12a; parakeet: gRNA; magenta: ssDNA trigger; pink: Mn²⁺