7YFC

Cryo-EM structure of the histamine-bound histamine H4 receptor and Gq complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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 insights into the agonists binding and receptor selectivity of human histamine H 4 receptor.

Im, D.Kishikawa, J.I.Shiimura, Y.Hisano, H.Ito, A.Fujita-Fujiharu, Y.Sugita, Y.Noda, T.Kato, T.Asada, H.Iwata, S.

(2023) Nat Commun 14: 6538-6538

  • DOI: https://doi.org/10.1038/s41467-023-42260-z
  • Primary Citation of Related Structures:  
    7YFC, 7YFD

  • PubMed Abstract: 

    Histamine is a biogenic amine that participates in allergic and inflammatory processes by stimulating histamine receptors. The histamine H 4 receptor (H 4 R) is a potential therapeutic target for chronic inflammatory diseases such as asthma and atopic dermatitis. Here, we show the cryo-electron microscopy structures of the H 4 R-G q complex bound with an endogenous agonist histamine or the selective agonist imetit bound in the orthosteric binding pocket. The structures demonstrate binding mode of histamine agonists and that the subtype-selective agonist binding causes conformational changes in Phe344 7.39 , which, in turn, form the "aromatic slot". The results provide insights into the molecular underpinnings of the agonism of H 4 R and subtype selectivity of histamine receptors, and show that the H 4 R structures may be valuable in rational drug design of drugs targeting the H 4 R.


  • Organizational Affiliation

    Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Engineered G-alpha-q361Homo sapiensMutation(s): 0 
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 
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP63096P63092
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1388Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16259Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Nb35E [auth N]129Lama glamaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histamine H4 receptorF [auth R]548Homo sapiensMutation(s): 0 
Gene Names: HRH4GPCR105
Membrane Entity: Yes 
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PHAROS:  Q9H3N8
GTEx:  ENSG00000134489 
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UniProt GroupQ9H3N8
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Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
HSM BindingDB:  7YFC Ki: min: 1, max: 219 (nM) from 12 assay(s)
Kd: min: 5, max: 16 (nM) from 2 assay(s)
EC50: min: 7.4, max: 79 (nM) from 10 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101079

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2023-11-22
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Database references