9JEQ | pdb_00009jeq

Cryo-EM structure of Histamine-bound Histamine receptor 3 H3R 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


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Literature

Decoding ligand recognition and constitutive activation of histamine H3 and H4 receptors.

Jin, S.S.Zhang, H.Yan, J.H.Wu, C.R.Cai, X.Q.Wu, K.Wang, M.W.Xu, H.E.Yang, D.H.Jiang, Y.

(2025) Acta Pharmacol Sin 

  • DOI: https://doi.org/10.1038/s41401-025-01633-4
  • Primary Citation of Related Structures:  
    9JED, 9JEQ, 9JG1

  • PubMed Abstract: 

    Histamine H3 receptor (H3R) and H4 receptor (H4R) are key members of the histamine receptor family, with H3R as a potential target for narcolepsy treatments and H4R as a candidate for next-generation antihistamines for inflammatory and allergic diseases. Although progress has been made in understanding the structure of histamine receptors, the detailed mechanisms of ligand recognition and receptor antagonism for H3R and H4R remain unclear. In this study, using cryo-electron microscopy, we present an inactive structure of H4R bound to a selective antagonist, adriforant, and two Gi-coupled structures of H3R and H4R in complex with histamine. Our structural and mutagenesis analyses provide insights into the selective binding of adriforant to H4R and the recognition of histamine across histamine receptors. Our findings also uncovered distinct antagonistic mechanisms for H3R and H4R and identified the role of aromatic amino acids on extracellular loop 2 in modulating the constitutive activity of H3R and H4R. These findings advance our knowledge of the functional modulation of histamine receptors, providing a foundation for the development of targeted therapeutics for neurological and immune-related disorders.


  • Organizational Affiliation
    • Lingang Laboratory, Shanghai, 200031, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1A [auth B]339Homo sapiensMutation(s): 0 
Gene Names: GNB1
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2B [auth G]58Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt
Find proteins for P63212 (Bos taurus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1C [auth A]352Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
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GTEx:  ENSG00000127955 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histamine H3 receptorD [auth R]445Homo sapiensMutation(s): 0 
Gene Names: HRH3GPCR97
Membrane Entity: Yes 
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PHAROS:  Q9Y5N1
GTEx:  ENSG00000101180 
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UniProt GroupQ9Y5N1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ScFv16E [auth S]251Mus musculusMutation(s): 0 
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release