9V6O

Cryo-EM structure of human kappa opioid receptor - G protein signaling complex bound with nalfurafine.

Summary for 9V6O

• Entry DOI: 10.2210/pdb9v6o/pdb
• EMDB information: 64947
• Descriptor: Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, ... (6 entities in total)
• Functional Keywords: signal transduction, membrane protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 5
• Total formula weight: 152507.06

Authors

Suno-Ikeda, C.,Takai, T.,Hirose, M.,Inoue, A.,Sugita, Y.,Kato, T.,Kobayashi, T.,Suno, R. (deposition date: 2025-05-27, release date: 2025-11-19)

Primary citation

Suno-Ikeda, C.,Nishikawa, R.,Suzuki, R.,Yokoi, S.,Iwata, S.,Takai, T.,Ogura, T.,Hirose, M.,Tokuda, A.,Katamoto, R.,Inoue, A.,Asai, E.,Kise, R.,Sugita, Y.,Kato, T.,Nagase, H.,Mitsutake, A.,Saitoh, T.,Katayama, K.,Inoue, A.,Kandori, H.,Kobayashi, T.,Suno, R.
Structural and dynamic insights into the biased signaling mechanism of the human kappa opioid receptor.
Nat Commun, 16:9392-9392, 2025

PubMed Abstract: The κ-opioid receptor (KOR) is a member of the G protein-coupled receptor (GPCR) family, modulating cellular responses through transducers such as G proteins and β-arrestins. G-protein-biased KOR agonists aim to retain analgesic and antipruritic actions while limiting aversion and sedation. Aiming to inform G-biased KOR agonist design, we analyze signaling-relevant residues from structural and dynamic views. Here we show, using multiple complementary methods, shared residues that determine β-arrestin recruitment by nalfurafine and U-50,488H. Cryo-electron microscopy structures of the KOR-G signaling complexes identify the ligand binding mode in the activated state. Vibrational spectroscopy reveals ligand-induced conformational changes. Cell-based mutant experiments pinpoint four amino acids (K227, C286, H291, and Y312; Ballesteros-Weinstein numbering is shown in superscript) that play crucial roles in β-arrestin recruitment. Furthermore, MD simulations revealed that the four mutants tend to adopt conformations with reduced β-arrestin recruitment activity. Our research findings provide a foundation for enhancing KOR-mediated therapeutic effects while minimizing unwanted side effects by targeting specific residues within the KOR ligand-binding pocket, including K227 and Y312, which have previously been implicated in biased signaling.

PubMed: 41152269
DOI: 10.1038/s41467-025-64882-1

Experimental method

ELECTRON MICROSCOPY (2.76 Å)