9WSX | pdb_00009wsx

Cryo-EM structure of endomorphin-1-muOR-arrestin2-Fab30 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
Mu-type opioid receptor,Vasopressin V2 receptorA [auth R]386Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Oprm1MorOprmAVPR2ADHRDIRDIR3V2R
UniProt & NIH Common Fund Data Resources
Find proteins for P30518 (Homo sapiens)
Explore P30518 
Go to UniProtKB:  P30518
PHAROS:  P30518
GTEx:  ENSG00000126895 
Find proteins for P42866 (Mus musculus)
Explore P42866 
Go to UniProtKB:  P42866
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42866P30518
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-arrestin-1B [auth C]393Bos taurusMutation(s): 0 
Gene Names: ARRB1
UniProt
Find proteins for P17870 (Bos taurus)
Explore P17870 
Go to UniProtKB:  P17870
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17870
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab30 heavy chainC [auth H]236synthetic constructMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab30 light chainD [auth L]216synthetic constructMutation(s): 0 
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  • Reference Sequence

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
endomorphin-1E [auth P]5synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A [auth R]L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A [auth R]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
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