Table 1.
The rmsd between predicted ICLs and ECLs and their native counterparts
Loop | GPCR | Loop sequence | Loop length, residue numbering | rmsd*, Å | rmsd†, Å (Mem) |
ECL1 | bRh | GYFVF | 5, (101–105) | 0.17 | |
A2Ar | STGFCAA | 7, (67–73) | 0.18 | ||
β1AR | GTWLWG | 6, (105–110) | 0.27 | ||
β2AR | KMWTF | 5, (97–101) | 0.12 | ||
ECL2 | bRh | VGWSRYIPEGMQCSCGIDYYTPHEETN | 27, (173–199) | 11.53 | 3.44 |
A2Ar | GWNNCGQ(PKEGKNH)SQGCGEGQVACLFEDVVP | 32, (142–173)‡ | 4.39 | ||
β1AR | MHWWRDEDPQALKCYQDPGCCDFVTN | 26, (179–204) | 1.59 | ||
β2AR | MHWYRATHQEAINCYAEETCCDFFTN | 26, (171–196) | 2.17 | ||
ECL3 | bRh | HQGSDFG | 7, (278–284) | 0.77 | |
A2Ar | CPDCSHAP | 8, (259–266) | 1.94 | 1.11 | |
β1AR | NRDLVP | 6, (316–321) | 0.50 | ||
β2AR | QDNLIR | 6, (299–304) | 0.23 | ||
ICL1 | bRh | HKKLRT | 6, (65–70) | 0.41 | |
A2Ar | NSNLQNV | 7, (34–40) | 0.35 | ||
β1AR | TQRLQT | 6, (69–74) | 0.78 | ||
β2AR | FERLQT | 6, (61–66) | 0.27 | ||
ICL2 | bRh | CKPMSNFRFG | 10, (140–149) | 5.79 | 2.86 |
A2Ar | RIPLRYNGLVT | 11, (107–117) | 4.15 | 2.63 | |
β1AR | ITSPFRYQSLMT | 12, (143–154) | 0.33 | ||
β2AR | SPFKYQSLLT | 10. (137–146) | 0.46 | ||
ICL3 | bRh | GQLVFTVKEAAAQQQESA | 18, (224–241) | 8.51 | 8.80 |
A2Ar | Insertion of T4 lysozyme | ||||
β1AR | Insertion of T4 lysozyme | ||||
β2AR | Insertion of T4 lysozyme |
The sequence of the six ICL and ECL loops of bovine rhodopsin, the human A2A adenosine receptor, turkey β1 adrenergic receptor, and human β2 adrenergic receptor are listed here, except for ICL3 of A2Ar, β1AR, and β2AR, which, for crystallization purposes, is partially replaced by a T4 lysozyme.
*The rmsds are all of structures procured with methods already existing in PLOP and a set of parameters optimized for GPCRs.
†Mem refers to the rmsd of the loop using the membrane method developed for this project.
‡ECL2 of A2Ar is missing seven crystallographic residues. The rmsd is calculated using the residues specified by the crystal structure; the missing residues are omitted in the calculation.