8Y45 image
Deposition Date 2024-01-30
Release Date 2024-11-27
Last Version Date 2024-11-27
Entry Detail
PDB ID:
8Y45
Title:
Cryo-EM structure of opioid receptor with biased agonist
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Mus musculus (Taxon ID: 10090)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.45 Å
Aggregation State:
CELL
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Delta-type opioid receptor
Gene (Uniprot):OPRD1
Chain IDs:A
Chain Length:325
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Gene (Uniprot):GNB1
Chain IDs:B
Chain Length:358
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Gene (Uniprot):GNG2
Chain IDs:E (auth: C)
Chain Length:71
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein G(i) subunit alpha-2
Gene (Uniprot):GNAI2
Chain IDs:C (auth: D)
Chain Length:355
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:scFv16
Chain IDs:D (auth: S)
Chain Length:266
Number of Molecules:1
Biological Source:Mus musculus
Ligand Molecules
Primary Citation
Cryo-EM structure of small-molecule agonist bound delta opioid receptor-G i complex enables discovery of biased compound.
Nat Commun 15 8284 8284 (2024)
PMID: 39333070 DOI: 10.1038/s41467-024-52601-1

Abstact

Delta opioid receptor (δOR) plays a pivotal role in modulating human sensation and emotion. It is an attractive target for drug discovery since, unlike Mu opioid receptor, it is associated with low risk of drug dependence. Despite its potential applications, the pharmacological properties of δOR, including the mechanisms of activation by small-molecule agonists and the complex signaling pathways it engages, as well as their relation to the potential side effects, remain poorly understood. In this study, we use cryo-electron microscopy (cryo-EM) to determine the structure of the δOR-Gi complex when bound to a small-molecule agonist (ADL5859). Moreover, we design a series of probes to examine the key receptor-ligand interaction site and identify a region involved in signaling bias. Using ADL06 as a chemical tool, we elucidate the relationship between the β-arrestin pathway of the δOR and its biological functions, such as analgesic tolerance and convulsion activities. Notably, we discover that the β-arrestin recruitment of δOR might be linked to reduced gastrointestinal motility. These insights enhance our understanding of δOR's structure, signaling pathways, and biological functions, paving the way for the structure-based drug discovery.

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