Table 2. RMSD Values of RyR2 Structural Featuresa.
| full model | central domain | transmembrane | S4S5L |
S6 helix |
|||
|---|---|---|---|---|---|---|---|
| 4099–4963 | 4099–4206 | 4485–4963 | 4731–4781 | 4746–4766 | 4839–4889 | 4859–4869 | |
| 4C | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| 4O | 7.2 | 5.0 | 5.7 | 8.5 | 5.1 | 3.0 | 0.3 |
| 1C3O | 5.0 | 6.1 | 8.0 | 1.1 | 0.7 | 1.5 | 0.3 |
| 1C3O-open-S4S5L | 8.7 | 4.7 | 3.9 | 5.0 | 6.1 | 2.7 | 0.3 |
| 1C3O-H4762P | 8.4 | 6.4 | 5.9 | 6.1 | 5.2 | 2.1 | 0.2 |
| 1C3O-HID | 6.2 | 7.2 | 3.6 | 0.5 | 0.4 | 1.6 | 0.1 |
| 1C3O-open-S4S5L-HID | 6.3 | 5.4 | 5.8 | 4.3 | 3.4 | 1.1 | 0.3 |
| 1C3O-open-S4S5L-H4762P | 7.2 | 5.8 | 7.5 | 3.4 | 5.6 | 3.5 | 0.2 |
The RMSD values of an alignment of various structural features in each model system with reference to the 4C system are shown. Only the stated residue sequence on each of the four RyR2 subunits was retained for each comparison; the remaining residues were removed from the PDB files before the alignment. The residue sequences correspond to: (1) our full model (residues 4099–4206 and 4485–4963), (2) the central domain/U-motif region (residues 4099–4206), (3) the transmembrane domain region (residues 4485–4963), (4) a 51-residue region that included the S4S5L (residues 4731–4781), (5) the S4S5L region that was transposed from the open to the closed state subunits when producing the 1C3O-open-S4S5L chimera models (residues 4746–4766), (6) a 51-residue region along the S6 helical bundle that included the central hydrophobic gate (residues 4839–4889), and (7) an 11-residue portion of the S6 helical bundle that included the central hydrophobic gate (4859–4869). A visual comparison of the aligned structures for the S4S5L (residues 4731–4781) is provided in Figure S11. The alignment and RMSD values were obtained using UCSF Chimera 1.15.