New insights into GPCR coupling and dimerisation from cryo-EM structures

Abstract

Over the past three years (2020-2022) more structures of GPCRs have been determined than in the previous twenty years (2000-2019), primarily of GPCR complexes that are large enough for structure determination by single-particle cryo-EM. This review will present some structural highlights that have advanced our molecular understanding of promiscuous G protein coupling, how a G protein receptor kinase and β-arrestins couple to GPCRs, and GPCR dimerisation. We will also discuss advances in the use of gene fusions, nanobodies, and F_ab fragments to facilitate the structure determination of GPCRs in the inactive state that, on their own, are too small for structure determination by single-particle cryo-EM.

Graphical abstract

Figure 1

Structural snapshots of promiscuous GPCR-G protein coupling. Structural superposition of the GCGR coupled to G_s (blue) and G_i1 (red) showing similarities in TM6 (a) and differences in ICL2 (b) [10]. Structural superposition of the CCK_AR coupled to G_q (green), G_i1 (red) and G_s (blue) showing similarities in TM6 position (c), differences in the ordering of ICL3 depending on the coupled G protein (d) and differences in the engagement mode of the α-subunit C-terminal ‘wavy hook’ for G_s vs G_q(e) [15,16].

Figure 2

Variations in coupling of arrestins and GRK2 to GPCRs. (a) Cryo-EM density (EMDB-23979) of rhodopsin coupled to GRK1 [33]. Density for the F_ab required for structure determination has been removed for clarity. (b) Cryo-EM density of β₁AR in a lipid nanodisc coupled to β-arrestin1 (EMDB-10515) [37]. Density for F_ab30 required for structure determination has been removed for clarity. (c) Superposition of β₁AR coupled to mini-G_s (purple; PDB code 7JJO [72]) and β₁AR (grey) coupled to β-arrestin1 (green; PDB code 6TKO [37]). (d) Different conformations of the GRK coupling helix and arrestin finger loop when coupled to different receptors. (e–g) Variation in the angle of arrestin coupled to different receptors (see main text for references): (e) a view perpendicular to the membrane plane; panels (f–g) are views parallel to the membrane plane in positions 1 and 2, respectively, as defined in panel (e). (h) Snake plots of bovine rhodopsin with amino acid residues within 3.9 Å (inclusive) of either GRK, G protein or arrestin coloured appropriately. PDB codes for the complexes are as follows: rhodopsin-GRK, 7MTB [••]; rhodopsin-G protein, 6OYA [73]; rhodopsin-arrestin, 5W0P [74]. The panels were made using GPCRdb [75].

Figure 3

Signalling routes in GPCR dimers. (a) Cryo-EM density of the apelin receptor (EMDB-32243) shows that there is sufficient room for only one G protein to couple per dimer, and the C-terminus of the adjacent protomer binds in the G protein-coupling cleft in an auto-inhibitory mechanism [52]. The dimer interface is shown by in the GABAB receptor dimer (EMDB-21534) is from the VFT domain of one protomer through the transmembrane helices of the adjacent protomer that can couple to G protein. The structures of two transmembrane helical bundles are not identical and the G protein coupling site forms only in one protomer [46,47]. The dimer interface is shown by the red box. (c) The Ste2 dimer (EMDB-11720) contains two protomers of identical conformation that are both capable of coupling to G proteins simultaneously, although one G protein is highly mobile, with the exception of the α5 helix that is ordered where it contacts the receptor [53]. The tilt of the G protein with respect to the receptor is over 50° different from that observed in G protein-coupling to Class A receptors, thus allowing two G proteins to couple simultaneously. The signalling pathways through the receptor are assumed to follow the paradigm of a monomeric receptor, however it is unclear whether both G proteins can signal to the same extent and there could be crosstalk between protomers across the dimer interface [54]. The dimer interface is shown by the red box.

Figure 4

Examples of strategies to determine structures of GPCR inactive states. (a) Cryo-EM density of ligand-free Smoothened (EMDB-27062) [69]. (b) Cryo-EM density (EMDB-25648) of the adenosine A_2A receptor with a BRIL insertion in ICL3 and bound to an anti-BRIL Fab fragment [69]. (c) Cryo-EM density (EMDB-26589) of the neurotensin receptor NTSR1 engineered to contain the H5-ICL3-H6 region of MOR and bound to the anti-MOR nanobody Nb6 [67]. (d) Cryo-EM density (EMDB-26590) of the histamine H₂ receptor engineered to contain the H5-ICL3-H6 region of MOR, bound to the anti-MOR nanobody Nb6 and the anti-nanobody F_ab (NabFab) [67]. Ligand density in the orthosteric binding pocket is shown above each receptor.