8YN5

Cryo-EM structure of histamine H3 receptor in complex with histamine and Gi


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of ligand recognition and activation of the histamine receptor family.

Zhang, X.Liu, G.Zhong, Y.N.Zhang, R.Yang, C.C.Niu, C.Pu, X.Sun, J.Zhang, T.Yang, L.Zhang, C.Li, X.Shen, X.Xiao, P.Sun, J.P.Gong, W.

(2024) Nat Commun 15: 8296-8296

  • DOI: https://doi.org/10.1038/s41467-024-52585-y
  • Primary Citation of Related Structures:  
    8YN2, 8YN3, 8YN4, 8YN5, 8YN6, 8YN7, 8YN8, 8YN9, 8YNA

  • PubMed Abstract: 

    Histamine is a biogenic amine that is critical in various physiological and pathophysiological processes, including but not limited to allergic reactions, wakefulness, gastric acid secretion and neurotransmission. Here, we determine 9 cryo-electron microscopy (cryo-EM) structures of the 4 histamine receptors in complex with four different G protein subtypes, with endogenous or synthetic agonists bound. Inside the ligand pocket, we identify key motifs for the recognition of histamine, the distinct binding orientations of histamine and three subpockets that facilitate the design of specific ligands. In addition, we also identify key residues responsible for the selectivity of immethridine. Moreover, we reveal distinct structural features as determinants of Gq vs. Gs or Gs vs. Gi coupling differences among the histamine receptors. Our study provides a structural framework for understanding the ligand recognition and G protein coupling of all 4 histamine receptors, which may facilitate the rational design of ligands targeting these receptors.


  • Organizational Affiliation

    Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China. xuz56@pitt.edu.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 4 
Gene Names: GNAI1
EC: 3.6.5
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-1376Homo 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 
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Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody fragment scFv16D [auth E]255synthetic constructMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histamine H3 receptorE [auth R]659Homo sapiensMutation(s): 0 
Gene Names: HRH3
Membrane Entity: Yes 
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Find proteins for Q9Y5N1 (Homo sapiens)
Explore Q9Y5N1 
Go to UniProtKB:  Q9Y5N1
PHAROS:  Q9Y5N1
GTEx:  ENSG00000101180 
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UniProt GroupQ9Y5N1
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2019YFA0904100
National Natural Science Foundation of China (NSFC)ChinaT2221005

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection
  • Version 1.3: 2024-11-27
    Changes: Data collection