8X63

CryoEM structure of the histamine H1 receptor-BRIL/Anti BRIL Fab complex with mepyramine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Molecular mechanism of antihistamines recognition and regulation of the histamine H 1 receptor.

Wang, D.Guo, Q.Wu, Z.Li, M.He, B.Du, Y.Zhang, K.Tao, Y.

(2024) Nat Commun 15: 84-84

  • DOI: https://doi.org/10.1038/s41467-023-44477-4
  • Primary Citation of Related Structures:  
    8X5X, 8X5Y, 8X63, 8X64

  • PubMed Abstract: 

    Histamine receptors are a group of G protein-coupled receptors (GPCRs) that play important roles in various physiological and pathophysiological conditions. Antihistamines that target the histamine H 1 receptor (H 1 R) have been widely used to relieve the symptoms of allergy and inflammation. Here, to uncover the details of the regulation of H 1 R by the known second-generation antihistamines, thereby providing clues for the rational design of newer antihistamines, we determine the cryo-EM structure of H 1 R in the apo form and bound to different antihistamines. In addition to the deep hydrophobic cavity, we identify a secondary ligand-binding site in H 1 R, which potentially may support the introduction of new derivative groups to generate newer antihistamines. Furthermore, these structures show that antihistamines exert inverse regulation by utilizing a shared phenyl group that inserts into the deep cavity and block the movement of the toggle switch residue W428 6.48 . Together, these results enrich our understanding of GPCR modulation and facilitate the structure-based design of novel antihistamines.


  • Organizational Affiliation

    Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027, Hefei, P. R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histamine H1 receptor,Soluble cytochrome b562A [auth B]438Homo sapiensEscherichia coliMutation(s): 2 
Gene Names: HRH1cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P35367 (Homo sapiens)
Explore P35367 
Go to UniProtKB:  P35367
PHAROS:  P35367
GTEx:  ENSG00000196639 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP35367P0ABE7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y5E (Subject of Investigation/LOI)
Query on Y5E

Download Ideal Coordinates CCD File 
B
mepyramine
C17 H23 N3 O
YECBIJXISLIIDS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Y5E BindingDB:  8X63 Ki: 4.5 (nM) from 1 assay(s)
IC50: 5.75 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2024-01-17
    Type: Initial release