Table 2.
Structural similarity of the transmembrane regions of selected GPCR structures.*
| PDB ID | IU19 | 1GZM | 2I37 | 3CAP | 2Z73 | 2VT4 | 2RH1 | 3D4S | 3EML |
|---|---|---|---|---|---|---|---|---|---|
| 1U19 | 0.39 | 0.9 | 1.7 | 1.4 | 4.1 | 3.4 | 3.3 | 2.7 | |
| 1GZM | 0.9 | 1.7 | 1.3 | 4.2 | 3.4 | 3.3 | 2.7 | ||
| 2I37 | 1.6 | 1.5 | 4.1 | 3.5 | 3.5 | 2.8 | |||
| 3CAP | 1.8 | 4.4 | 3.4 | 3.4 | 3.1 | ||||
| 2Z73 | 4.1 | 3.2 | 3.2 | 3.1 | |||||
| 2VT4† | 5.8 | 5.8 | 4.2 | ||||||
| 2RH1 | 0.36 | 4.4 | |||||||
| 3D4S | 4.3 | ||||||||
| 3EML |
The pairwise root mean squared deviations (RMSDs) of the transmembrane regions of rhodopsin, opsin and adrenergic receptors were calculated. Transmembrane regions were determined by homology to the transmembrane regions of bovine rhodopsin in the cases of the adrenergic receptors and squid rhodopsin. While RMSDs of all rhodopsin transmembrane regions are within 1.8 Å, the adrenergic receptors superpose more poorly (3.3-3.5 Å for β2 and 4.1-4.4 for β1). Surprisingly, β1-adrenergic receptor and β2-adrenergic receptor superpose better onto rhodopsin than they do onto one another. PDB codes for the structure superpositions: ground state rhodopsin, 1U19 and 1GZM (30,33); photoactivated rhodopsin, 2I37 (15); opsin, 3CAP(16); squid rhodopsin, 2Z73 (36); β1-adrenergic receptor, 2VT4(48); β2-adrenergic receptor, 2RH1 and 3D4S (17,49); A2A-adenosine receptor, 3EML(54). RMSDs were calculated with the program SUPERPOSE, using the following transmembrane segments of rhodopsin and homologous regions of the other GPCRs: H-I; 36-64, H-II; 72-100, H-III; 107-139, H-IV; 149-173, H-V 200-228, H-VI; 246-276, H-VII; 286-306.
In structures containing more than one GPCR, monomer A was utilized for comparisons, with the exception of the β1-adrenergic receptor monomer B was used because monomer A contains a bend in H-I which is not expected to exist physiologically.