Figure 3.

Localization of the IP₃-like region of RyR1. (a) Homology model for the InP₃-like RyR1 domain (blue/red ribbon) and corresponding 14 Å density map (transparent red) generated using EMAN. The sequence corresponding to the LZ1 region residues 541–572 is shown with red ribbon. A homology model was generated by mapping of the coordinates of the X-ray structure of the IP₃-binding core region (1N4K)²⁰ and the sequence residues 216–572 of RyR1 aligned to them. The model was further enhanced by the addition of side-chains using the SCWL algorithm.³⁰ Sequence alignment, secondary structure prediction and homology modeling were performed using 3D-PSSM Fold Recognition server. (b) Fitting of 14 Å electron density map of the IP₃-like domain within RyR1 tetramer shown in tilted stereo top-view. Assignment of mass densities for the IP₃-like domain was performed using 6D fitting program Foldhunter as previously described.³ The top four correlation peaks with local correlation coefficients of about 0.91 (Foldhunter score) are found in the clamp-shaped domain of each of the four monomers in the RyR1 reconstruction. This fit had a z-score of 1.97. z-Score is a statistical measure of the number of standard deviations from the mean, which, in this case, corresponds a confidence level greater than 95%. A star marks the C terminus of the modeled region.