Cryo-EM structure of the human histamine H1 receptor/Gq complex

Abstract

Histamine receptors play important roles in various pathophysiological conditions and are effective targets for anti-allergy treatment, however the mechanism of receptor activation remain elusive. Here, we present the cryo-electron microscopy (cryo-EM) structure of the human H₁R in complex with a G_q protein in an active conformation via a NanoBiT tethering strategy. The structure reveals that histamine activates receptor via interacting with the key residues of both transmembrane domain 3 (TM3) and TM6 to squash the binding pocket on the extracellular side and to open the cavity on the intracellular side for G_q engagement in a model of "squash to activate and expand to deactivate". The structure also reveals features for G_q coupling, including the interaction between intracellular loop 2 (ICL2) and the αN-β junction of G_q/11 protein. The detailed analysis of our structure will provide a framework for understanding G-protein coupling selectivity and clues for designing novel antihistamines.

Fig. 1. Overall structure of the H₁R/G_q complex.

a Orthogonal views of the cryo-EM density map of the H₁R/G_q complex. b Model of the complex in same view and color scheme as shown in (a). HSM: histamine.

Fig. 2. Histamine binding and the ligand-binding pocket.

a The ligand-binding pocket of histamine. The histamine is shown in red in the middle of the pocket, density map of histamine (blue mesh) is set at contour level of 3.0. Surrounding residues within 4.1 Å of histamine are shown in sticks and colored in cyan. Hydrogen bonds are marked as yellow dash line. b A NFAT-RE reporter assay of mutations of key residues in the ligand-binding pocket. Histamine, 10 µM; data are presented as mean values ± SD; n = 3 independent samples. RLU, relative luciferase unit. WT, wild-type. c The electrostatic potential surface of H₁R and the histamine binding pocket. The chemical structure of histamine is shown on the up-right panel.

Fig. 3. Activation of H₁R by the binding of histamine.

a A comparison of histamine-bound active H₁R and the inverse agonist doxepin-bound inactive H₁R (PDB 3RZE). The helices are shown in cylinders. Active receptor is shown in cyan and inactive receptor is shown in light pink. Up-panel is the extracellular side view and lower-panel is the intracellular side view. Arrows mark the movement of the designate part of receptor upon histamine binding. b A comparison of the agonist (histamine) binding pocket (cyan) with the inverse agonist (doxepin) binding pocket (light pink). The cyan arrow marks the movements of key residues on TM6 upon agonist (histamine) binding and the light pink arrow marks the movements of key residues on TM6 upon inverse agonist (doxepin) binding. c The movements of TM6 upon receptor activation. The W428^6.48 severs as a pivot between the upside (extracelluar) movement and the downside movement of TM6. d A simple model (for illustration only) of a designed salt bridge interaction between the Y431R mutation of TM6 and with the negative charge D107^3.32 of TM3. e A NFAT-RE reporter assay of the Y431^6.51 and D107^3.32 mutations. Histamine, 10 µM; data are presented as mean values ± SD; n = 3 independent samples. RLU, relative luciferase unit.

Fig. 4. The engagement G_q to H₁R.

a The interaction between the receptor and the αH5, viewing from the TM6, TM7-H8 front angle. The receptor is colored in cyan and Gα_q is colored in orange. b The interaction between the receptor and Gα_q, viewing from the TM5, TM3, and ICL2 front angle. c the ICL2/Gβ interaction. The receptor is colored in cyan and Gβ is colored in slate. Density map of designated region is set to contour level of 3.0. d An overall comparison of the H₁R/G_q complex with the M1R/G₁₁ complex (PDB 6OIJ). e A comparison of the engagement of αH5 to receptor between the H₁R/G_q complex with the M1R/G₁₁ complex. f A comparison of the αN displacements of G_q/11 in receptor engagement. M1R/G₁₁ (PDB 6OIJ), HT2AR/mini-G_q (PDB 6WHA) and GDP-bound G_q (PDB 3AH8).

Fig. 5. Comparisons of G_q-coupled H₁R with G_s- and G_i-coupled receptors.

a A comparison of the αH5 engagement between GLP-1R/G_s (PDB 5VAI) and the H₁R/G_q complex. The dashed arrow shows the additional outward displacement of the TM6 of GLP-1R. b A comparison of the Gβ interactions between the CTR/G_s (PDB 5UZ7). c A comparison of the ICL2 interaction between the DRD2/G_i (PDB 6VMS) and the H₁R/G_q complex.