8YN9

Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 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 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, 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)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups  
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UniProt GroupP63096
Sequence Annotations
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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)
Explore P62873 
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 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
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 H4 receptorE [auth R]638Homo sapiensMutation(s): 0 
Gene Names: HRH4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3N8 (Homo sapiens)
Explore Q9H3N8 
Go to UniProtKB:  Q9H3N8
PHAROS:  Q9H3N8
GTEx:  ENSG00000134489 
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UniProt GroupQ9H3N8
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
G [auth R]
H [auth R]
I [auth R]
J [auth R]
K [auth R]
G [auth R],
H [auth R],
I [auth R],
J [auth R],
K [auth R],
L [auth R],
M [auth R]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
HSM (Subject of Investigation/LOI)
Query on HSM

Download Ideal Coordinates CCD File 
F [auth R]HISTAMINE
C5 H9 N3
NTYJJOPFIAHURM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



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