8K9L

Full agonist- and positive allosteric modulator-bound mu-type opioid receptor-G protein complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural and dynamic insights into the activation of the mu-opioid receptor by an allosteric modulator.

Kaneko, S.Imai, S.Uchikubo-Kamo, T.Hisano, T.Asao, N.Shirouzu, M.Shimada, I.

(2024) Nat Commun 15: 3544-3544

  • DOI: https://doi.org/10.1038/s41467-024-47792-6
  • Primary Citation of Related Structures:  
    8K9K, 8K9L

  • PubMed Abstract: 

    G-protein-coupled receptors (GPCRs) play pivotal roles in various physiological processes. These receptors are activated to different extents by diverse orthosteric ligands and allosteric modulators. However, the mechanisms underlying these variations in signaling activity by allosteric modulators remain largely elusive. Here, we determine the three-dimensional structure of the μ-opioid receptor (MOR), a class A GPCR, in complex with the G i protein and an allosteric modulator, BMS-986122, using cryogenic electron microscopy. Our results reveal that BMS-986122 binding induces changes in the map densities corresponding to R167 3.50 and Y254 5.58 , key residues in the structural motifs conserved among class A GPCRs. Nuclear magnetic resonance analyses of MOR in the absence of the G i protein reveal that BMS-986122 binding enhances the formation of the interaction between R167 3.50 and Y254 5.58 , thus stabilizing the fully-activated conformation, where the intracellular half of TM6 is outward-shifted to allow for interaction with the G i protein. These findings illuminate that allosteric modulators like BMS-986122 can potentiate receptor activation through alterations in the conformational dynamics in the core region of GPCRs. Together, our results demonstrate the regulatory mechanisms of GPCRs, providing insights into the rational development of therapeutics targeting GPCRs.


  • Organizational Affiliation

    Center for Biosystems Dynamics Research (BDR), RIKEN, Kanagawa, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Mu-type opioid receptor,Mu-type opioid receptorA [auth R]453Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: cybCOPRM1MOR1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P35372 (Homo sapiens)
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PHAROS:  P35372
GTEx:  ENSG00000112038 
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UniProt GroupP35372
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DAMGOB [auth S]5synthetic constructMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
G protein subunit alpha i3C [auth A]354Macaca mulattaMutation(s): 0 
Gene Names: GNAI3
UniProt
Find proteins for F6VL43 (Macaca mulatta)
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UniProt GroupF6VL43
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1D [auth B]348Homo 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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [auth G]72Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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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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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16F [auth H]257synthetic constructMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VV9 (Subject of Investigation/LOI)
Query on VV9

Download Ideal Coordinates CCD File 
G [auth R](2~{S})-2-(3-bromanyl-4-methoxy-phenyl)-3-(4-chlorophenyl)sulfonyl-1,3-thiazolidine
C16 H15 Br Cl N O3 S2
PNGJPVDGZNPZHY-INIZCTEOSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEA
Query on MEA
B [auth S]L-PEPTIDE LINKINGC10 H13 N O2PHE
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP17H06097
Japan Society for the Promotion of Science (JSPS)JapanJP21H02619
Japan Society for the Promotion of Science (JSPS)JapanJP23KJ0574
Japan Agency for Medical Research and Development (AMED)Japan21ae0121028h0001

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release