8JXT

Histamine-bound H4R/Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 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 design of antihistamines targeting histamine H 4 receptor.

Xia, R.Shi, S.Xu, Z.Vischer, H.F.Windhorst, A.D.Qian, Y.Duan, Y.Liang, J.Chen, K.Zhang, A.Guo, C.Leurs, R.He, Y.

(2024) Nat Commun 15: 2493-2493

  • DOI: https://doi.org/10.1038/s41467-024-46840-5
  • Primary Citation of Related Structures:  
    8JXT, 8JXV, 8JXW, 8JXX

  • PubMed Abstract: 

    The histamine H 4 receptor (H 4 R) plays key role in immune cell function and is a highly valued target for treating allergic and inflammatory diseases. However, structural information of H 4 R remains elusive. Here, we report four cryo-EM structures of H 4 R/G i complexes, with either histamine or synthetic agonists clobenpropit, VUF6884 and clozapine bound. Combined with mutagenesis, ligand binding and functional assays, the structural data reveal a distinct ligand binding mode where D94 3.32 and a π-π network determine the orientation of the positively charged group of ligands, while E182 5.46 , located at the opposite end of the ligand binding pocket, plays a key role in regulating receptor activity. The structural insight into H 4 R ligand binding allows us to identify mutants at E182 5.46 for which the agonist clobenpropit acts as an inverse agonist and to correctly predict inverse agonism of a closely related analog with nanomolar potency. Together with the findings regarding receptor activation and G i engagement, we establish a framework for understanding H 4 R signaling and provide a rational basis for designing novel antihistamines targeting H 4 R.


  • Organizational Affiliation

    Laboratory of Receptor Structure and Signaling, HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1A [auth B]354Homo sapiensMutation(s): 2 
Gene Names: GNAI1
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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63096
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1B [auth C]345Homo 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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62873
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth D]71Homo 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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59768
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16D [auth E]247Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histamine H4 receptorE [auth R]390Homo sapiensMutation(s): 0 
Gene Names: HRH4GPCR105
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H3N8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
HSM BindingDB:  8JXT 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: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2024-03-20 
  • Deposition Author(s): He, Y., Xia, R.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32070048

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Database references