9JG1 | pdb_00009jg1

Cryo-EM structure of Adriforant-bound Histamine receptor 4 H4R at inactive state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9JG1

This is version 1.1 of the entry. See complete history

Literature

Decoding ligand recognition and constitutive activation of histamine H3 and H4 receptors.

Jin, S.S.Zhang, H.Yan, J.H.Wu, C.R.Cai, X.Q.Wu, K.Wang, M.W.Xu, H.E.Yang, D.H.Jiang, Y.

(2026) Acta Pharmacol Sin 47: 186-196

  • DOI: https://doi.org/10.1038/s41401-025-01633-4
  • Primary Citation Related Structures: 
    9JED, 9JEQ, 9JG1

  • PubMed Abstract: 

    Histamine H3 receptor (H3R) and H4 receptor (H4R) are key members of the histamine receptor family, with H3R as a potential target for narcolepsy treatments and H4R as a candidate for next-generation antihistamines for inflammatory and allergic diseases. Although progress has been made in understanding the structure of histamine receptors, the detailed mechanisms of ligand recognition and receptor antagonism for H3R and H4R remain unclear. In this study, using cryo-electron microscopy, we present an inactive structure of H4R bound to a selective antagonist, adriforant, and two Gi-coupled structures of H3R and H4R in complex with histamine. Our structural and mutagenesis analyses provide insights into the selective binding of adriforant to H4R and the recognition of histamine across histamine receptors. Our findings also uncovered distinct antagonistic mechanisms for H3R and H4R and identified the role of aromatic amino acids on extracellular loop 2 in modulating the constitutive activity of H3R and H4R. These findings advance our knowledge of the functional modulation of histamine receptors, providing a foundation for the development of targeted therapeutics for neurological and immune-related disorders.


  • Organizational Affiliation
    • Lingang Laboratory, Shanghai, 200031, China.

Macromolecule Content 

  • Total Structure Weight: 97.53 kDa 
  • Atom Count: 4,730 
  • Modeled Residue Count: 613 
  • Deposited Residue Count: 875 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histamine H4 receptor,Soluble cytochrome b562A [auth R]427Homo sapiensEscherichia coliMutation(s): 0 
Gene Names: HRH4GPCR105cybC
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
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 GroupsP0ABE7Q9H3N8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-BRIL Fab Heavy chainB [auth H]222Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-BRIL Fab Light chainC [auth L]226Homo sapiensMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EBW
(Subject of Investigation/LOI)

Query on A1EBW



Download:Ideal Coordinates CCD File
D [auth R]Adriforant
C13 H22 N6
ISBHYKVAFKTATD-SNVBAGLBSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2026-01-21
    Changes: Data collection, Database references