9WST | pdb_00009wst

Cryo-EM structure of DAMGO-muOR-Gz-scFv16 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The molecular basis of mu-opioid receptor signaling plasticity.

Zhang, H.Wang, X.Xi, K.Shen, Q.Xue, J.Zhu, Y.Zang, S.K.Yu, T.Shen, D.D.Guo, J.Chen, L.N.Ji, S.Y.Qin, J.Dong, Y.Zhao, M.Yang, M.Wu, H.Yang, G.Zhang, Y.

(2025) Cell Res 35: 1021-1036

  • DOI: https://doi.org/10.1038/s41422-025-01191-8
  • Primary Citation of Related Structures:  
    9WST, 9WSV, 9WSW, 9WSX

  • PubMed Abstract: 

    Activation of the μ-opioid receptor (μOR) alleviates pain but also elicits adverse effects through diverse G proteins and β-arrestins. The structural details of μOR complexes with G z and β-arrestins have not been determined, impeding a comprehensive understanding of μOR signaling plasticity. Here, we present the cryo-EM structures of the μOR-G z and μOR-βarr1 complexes, revealing selective conformational preferences of μOR when engaged with specific downstream signaling transducers. Integrated receptor pharmacology, including high-resolution structural analysis, cell signaling assays, and molecular dynamics simulations, demonstrated that transmembrane helix 1 (TM1) acts as an allosteric regulator of μOR signaling bias through differential stabilization of the G i -, G z -, and βarr1-bound states. Mechanistically, outward TM1 displacement confers structural flexibility that promotes G protein recruitment, whereas inward TM1 retraction facilitates βarr1 recruitment by stabilizing the intracellular binding pocket through coordinated interactions with TM2, TM7, and helix8. Structural comparisons between the G i -, G z -, and βarr1-bound complexes identified a TM1-fusion pocket with significant implications for downstream signaling regulation. Overall, we demonstrate that the conformational and thermodynamic heterogeneity of TM1 allosterically drives the downstream signaling specificity and plasticity of μOR, thereby expanding the understanding of μOR signal transduction mechanisms and providing new avenues for the rational design of analgesics.


  • Organizational Affiliation
    • Department of Pathology of Sir Run Run Shaw Hospital, Department of Pharmacology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Engineered guanine nucleotide-binding protein G(z) subunit alpha355Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1371Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
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-2C [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mu-type opioid receptor,LgBiTD [auth R]575Homo sapiensOplophorus gracilirostris
This entity is chimeric
Mutation(s): 0 
Gene Names: OPRM1MOR1
UniProt & NIH Common Fund Data Resources
Find proteins for P35372 (Homo sapiens)
Explore P35372 
Go to UniProtKB:  P35372
PHAROS:  P35372
GTEx:  ENSG00000112038 
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UniProt GroupP35372
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DAMGOE [auth P]5synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEA
Query on MEA
E [auth P]L-PEPTIDE LINKINGC10 H13 N O2PHE
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Data collection, Database references