Hypothetical homotetramer structure of RYR1 after the MD simulation. (A–B) The hypothetical homotetramer of the crystal structure of the RYR1 NTD (2XOA; Tung et al., 2010) (A) and the structure in the WT after 50 ns of the MD simulation (B) are represented by a ribbon and surface model. To create a hypothetical homotetramers of the NTDs, monomer structures are fitted to the cryo-EM structure of RYR1 in the closed state (5TB0). The blue dotted circle indicates the diameter of the central orifice. The radius of both circles shown in A and B is almost the same (~ 27 Å). (C–D) Hypothetical homotetramers of the R402C (C) and R402H (D) after 50 ns of the MD simulation. To create hypothetical homotetramers of the NTDs, mutants after the MD simulation were fitted to the cryo-EM structure in closed state using A domain in the NTD. The position of the mutated residue was indicated by green as the space filling model. Red dotted circles indicate the diameter of the central orifice in the R402C (~ 34 Å) and R402H (~ 36 Å) mutants, respectively. The blue dotted circle indicates the diameter of the central orifice shown in A and B (~ 27 Å). In the R402C/H mutations, the size of the central orifice becomes larger than that in the WT. (E) Comparison of the NTD of the cryo-EM structure in the closed (5TB0) and open (5T9V) state of RYR1. Blue and red circles indicate the diameter of the central orifice in closed (~ 24 Å) and open states (~ 29 Å), respectively. In the open state, the size of the central orifice becomes larger than that in the closed state. (F) Superimposition of the monomers of the cryo-EM structures in the closed state and open state. The monomer of the NTD in the open state was fitted to the A domain of the NTD in the closed state. (G) Superimposition of NTD of the cryo-EM structures in the closed state (light orange) and open state (red) is represented by the ribbon model. The structure in the open state is shown as a monomer. The NTD translationally moves 3.6 Å, as indicated by the arrow.