9PXU image
Deposition Date 2025-08-06
Release Date 2025-11-12
Last Version Date 2025-11-19
Entry Detail
PDB ID:
9PXU
Title:
Inactive-state naloxone-mu opioid receptor nanobody6 complex
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Nanobody6
Chain IDs:B (auth: C)
Chain Length:131
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Molecule:Nab-fab heavy chain
Chain IDs:E (auth: H)
Chain Length:239
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Molecule:Anti-fab nanobody
Chain IDs:C (auth: K)
Chain Length:126
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Molecule:Nab-fab light chain
Chain IDs:D (auth: L)
Chain Length:215
Number of Molecules:1
Biological Source:synthetic construct
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Soluble cytochrome b562,Mu-type opioid receptor
Gene (Uniprot):cybC, OPRM1
Chain IDs:A (auth: R)
Chain Length:622
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Structural snapshots capture nucleotide release at the mu-opioid receptor.
Nature ? ? ? (2025)
PMID: 41193810 DOI: 10.1038/s41586-025-09677-6

Abstact

As a member of the G protein-coupled receptor superfamily, the μ-opioid receptor (MOR) activates heterotrimeric G proteins by opening the Gα α-helical domain (AHD) to enable GDP-GTP exchange, with GDP release representing the rate-limiting step1,2. Here, using pharmacological assays, we show that agonist efficacy correlates with decreased GDP affinity, promoting GTP exchange, whereas antagonists increase GDP affinity, dampening activation. Further investigating this phenomenon, we provide 8 unique structural models and 16 cryogenic electron microscopy maps of MOR with naloxone or loperamide, capturing several intermediate conformations along the activation pathway. These include four GDP-bound states with previously undescribed receptor-G protein interfaces, AHD arrangements and transitions in the nucleotide-binding pocket required for GDP release. Naloxone stalls MOR in a 'latent' state, whereas loperamide promotes an 'engaged' state, which is structurally poised for opening of the AHD domain and subsequent GDP release. These findings, supported by molecular dynamics simulations, identify GDP-bound intermediates and AHD conformations as key determinants of nucleotide exchange rates, providing structural and mechanistic insights into G protein activation and ligand efficacy with broad implications for G protein-coupled receptor pharmacology.

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Primary Citation of related structures
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