7T2G

CryoEM structure of mu-opioid receptor - Gi protein complex bound to mitragynine pseudoindoxyl (MP)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Insights into distinct signaling profiles of the mu OR activated by diverse agonists.

Qu, Q.Huang, W.Aydin, D.Paggi, J.M.Seven, A.B.Wang, H.Chakraborty, S.Che, T.DiBerto, J.F.Robertson, M.J.Inoue, A.Suomivuori, C.M.Roth, B.L.Majumdar, S.Dror, R.O.Kobilka, B.K.Skiniotis, G.

(2022) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-022-01208-y
  • Primary Citation of Related Structures:  
    7T2G, 7T2H

  • PubMed Abstract: 

    Drugs targeting the μ-opioid receptor (μOR) are the most effective analgesics available but are also associated with fatal respiratory depression through a pathway that remains unclear. Here we investigated the mechanistic basis of action of lofentanil (LFT) and mitragynine pseudoindoxyl (MP), two μOR agonists with different safety profiles. LFT, one of the most lethal opioids, and MP, a kratom plant derivative with reduced respiratory depression in animal studies, exhibited markedly different efficacy profiles for G protein subtype activation and β-arrestin recruitment. Cryo-EM structures of μOR-Gi1 complex with MP (2.5 Å) and LFT (3.2 Å) revealed that the two ligands engage distinct subpockets, and molecular dynamics simulations showed additional differences in the binding site that promote distinct active-state conformations on the intracellular side of the receptor where G proteins and β-arrestins bind. These observations highlight how drugs engaging different parts of the μOR orthosteric pocket can lead to distinct signaling outcomes.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
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Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1344Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-271Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
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Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Mu-type opioid receptorD [auth R]488Escherichia coliMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: cybCOprm1MorOprm
Membrane Entity: Yes 
UniProt
Find proteins for P42866 (Mus musculus)
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Go to UniProtKB:  P42866
Find proteins for P0ABE7 (Escherichia coli)
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Go to UniProtKB:  P0ABE7
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UniProt GroupsP0ABE7P42866
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS092695

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2022-12-14
    Changes: Database references
  • Version 2.0: 2023-02-15
    Type: Coordinate replacement
    Reason: Missing anisotropic B-factor
    Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary