Fig. 1.

Pseudo-symmetric domains formed from 3/4TMH protodomains—see main text for explanations. Color coding of the TM helices in each 3TMH protodomain with BLUE, MAGENTA, and ORANGE, as mentioned in the methods section, enables a quick equivalence between the individual helices from each protodomain. For example, the first and second 3TMH protodomains of a GPCR (TM1–TM2–TM3 and TM5–TM6–TM7, respectively) are colored as TM1/TM5 in BLUE, TM2/TM6 in MAGENTA, and TM3/7 in ORANGE, showing the equivalence of the TM helix pairs TM1–TM5, TM2–TM6, and TM3–TM7. GRAY is used for an additional helix in 7TMH and for the 4th helix in 4TMH protodomains. RMSD reported for optimized structural alignment of protodomains (see Methods). In the case of PnuC, a 3TMH alignment leads to 1.26 Å, while for 4TMH it rises to 3.09 Å (including TM0/TM4—see text for more details). The iCn3D links for the PDB ids are available in the online version as: 4QNC/4QND, 5CTH, 4QTN, 4OR2, 5WUF, 3KCU, 3NE2, 5EQI