9LRB | pdb_00009lrb

Cryo-EM structure of the histamine H1 receptor-Gs protein complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 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

Structural insights into ligand recognition and G protein preferences across histamine receptors.

Matsuzaki, Y.Sano, F.K.Oshima, H.S.Akasaka, H.Kobayashi, K.Tanaka, T.Itoh, Y.Shihoya, W.Kise, Y.Kusakizako, T.Inoue, A.Nureki, O.

(2025) Commun Biol 8: 957-957

  • DOI: https://doi.org/10.1038/s42003-025-08363-7
  • Primary Citation of Related Structures:  
    9LRB, 9LRC, 9LRD, 9LRE

  • PubMed Abstract: 

    Histamine exerts critical physiological roles by activating four receptor subtypes, each exhibiting a specific G protein preference. Among these, the histamine H 4 receptor (H 4 R) modulates chemotaxis and interferon production through G i protein activation, suggesting its therapeutic potential. Despite its physiological significance, the mechanisms underlying H 4 R signalling and G protein preference across histamine receptors remain poorly understood. Here, we present the cryo-electron microscopy structure of the H 4 R-G i complex, revealing unique mechanisms of histamine recognition and receptor activation. We further solved the structures of the histamine H 1 receptor (H 1 R) bound to the non-canonical G proteins G i and G s . Through a combination of functional and computational analyses, we identified the intracellular loop 2 as a critical determinant of G protein preference in H 1 R and H 4 R. Collectively, our comprehensive study revealed the structural basis for distinct mechanisms of ligand recognition and receptor activation, offering a profound insight into G protein preference across receptor subtypes.


  • Organizational Affiliation
    • Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short249Homo sapiensMutation(s): 0 
Gene Names: GNASGNAS1GSP
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
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PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupP63092
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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-1351Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus)
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UniProt GroupP54311
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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]68Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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UniProt GroupP63212
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
nanobody 35D [auth N]137unidentifiedMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histamine H1 receptor,Genome polyproteinE [auth R]802Homo sapiensMutation(s): 0 
Gene Names: HRH1
Membrane Entity: Yes 
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Find proteins for P35367 (Homo sapiens)
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Go to UniProtKB:  P35367
PHAROS:  P35367
GTEx:  ENSG00000196639 
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UniProt GroupP35367
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Data collection, Database references