9WP9

Cryo-EM structure of the d18:1 S1P-bound S1PR3 and Gq complex

Summary for 9WP9

• Entry DOI: 10.2210/pdb9wp9/pdb
• EMDB information: 66136
• Descriptor: Engineered G-alpha-q, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, scFv16, ... (7 entities in total)
• Functional Keywords: gpcr, sbdd, lipid, membrane protein
• Biological source: Homo sapiens; More
• Total number of polymer chains: 6
• Total formula weight: 155969.76

Authors

Im, D.,Asada, H.,Iwata, S.,Yamauchi, M.,Hagiwara, M. (deposition date: 2025-09-08, release date: 2025-11-26)

Primary citation

Yamauchi, M.,Im, D.,Maeda, S.,Ikuta, T.,Toyomoto, M.,Asada, H.,Sugita, Y.,Kishikawa, J.I.,Noda, T.,Kato, T.,Inoue, A.,Iwata, S.,Hagiwara, M.
Structural insights into the G-protein subtype selectivity revealed by human sphingosine-1-phosphate receptor 3-G q complexes.
Proc.Natl.Acad.Sci.USA, 122:e2507421122-e2507421122, 2025

PubMed Abstract: Sphingosine-1-phosphate (S1P) is one of the most extensively studied bioactive lipids that transduces signals via the S1P receptor (S1PR) family (S1PR1-5), a class of G-protein-coupled receptors (GPCRs), to regulate immune cell migration, vascular permeability, and pain modulation. However, the mechanism for achieving specificity in downstream signaling remains poorly understood. Here, we present cryogenic electron microscopic structures of the S1PR3-G complex bound to endogenous agonists: d18:1 S1P or d16:1 S1P. Both agonists shared the same binding pocket and binding mode despite the different signaling intensities of the S1PR3-G signal pathway. By comparing the structures of two agonist-bound complexes, combined with mutagenesis studies, we identified key amino acids, Phe119 and Arg136, that play crucial roles in differential agonist recognition and receptor activation. Furthermore, structural comparisons with previously determined S1PR3-G complex or G-protein-free S1PR3 structures, along with mutagenesis analysis, revealed dynamic intracellular loop 2 conformations and specific amino acid interactions that contribute to G-protein selectivity. Notably, we identified amino acids at the 34.50 and 34.53 positions within ICL2 as critical for specific interactions with G proteins. These findings provide better understanding of the mechanism of GPCR activation and unique perspectives that can be applied to other class A GPCRs, leading to the possibility of optimized drug development.

PubMed: 41252158
DOI: 10.1073/pnas.2507421122

Experimental method

ELECTRON MICROSCOPY (3.25 Å)