9UWD | pdb_00009uwd

Cryo-EM structure of inactive-DP1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 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

Molecular basis for ligand recognition and receptor activation of the prostaglandin D2 receptor DP1.

Xu, J.Wu, Y.Xu, Y.Li, Y.He, X.Zhang, H.Wang, J.J.Hou, J.Li, J.Hu, W.Wu, K.Yuan, Q.Wu, C.Xu, H.E.

(2025) Proc Natl Acad Sci U S A 122: e2501902122-e2501902122

  • DOI: https://doi.org/10.1073/pnas.2501902122
  • Primary Citation of Related Structures:  
    8ZVZ, 8ZW0, 9UWD

  • PubMed Abstract: 

    The prostaglandin D2 receptor 1 (DP1), a rhodopsin-like Class A GPCR, orchestrates critical physiological and pathological processes, ranging from sleep regulation to inflammatory responses and cardiovascular function. Despite its therapeutic significance, structural insights into DP1 activation mechanisms have remained elusive. Here, using cryoelectron microscopy (cryo-EM), we determined high-resolution structures of human DP1 in both inactive and active states, with the latter captured in complex with its endogenous agonist PGD2 or the synthetic agonist BW245C, bound to the stimulatory G protein, Gs. Our structures, coupled with functional and mutagenesis studies, unveiled unique structural features of DP1, including an alternative activation mechanism, ligand-selectivity determinants, and G protein coupling characteristics. These molecular insights provide a rational framework for designing selective DP1-targeted therapeutics, both agonists and antagonists, with enhanced specificity and reduced off-target effects, opening broad avenues for treating DP1-associated disorders.


  • Organizational Affiliation
    • State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prostaglandin D2 receptor,Soluble cytochrome b562428Homo sapiensEscherichia coliMutation(s): 0 
Gene Names: PTGDRcybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13258 (Homo sapiens)
Explore Q13258 
Go to UniProtKB:  Q13258
PHAROS:  Q13258
GTEx:  ENSG00000168229 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13258
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 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: 2025-05-28
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Data collection, Database references