8ZW0 image
Deposition Date 2024-06-12
Release Date 2025-05-28
Last Version Date 2025-06-25
Entry Detail
PDB ID:
8ZW0
Title:
Cryo-EM strcuture of Prostaglandin D2 Receptor DP1 activated by PGD2
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Escherichia coli (Taxon ID: 562)
Lama glama (Taxon ID: 9844)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.72 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Gene (Uniprot):GNAS
Mutations:S54N,G226A,E268A,N271K,K274D,R280K,T284D,I285T,A366S
Chain IDs:A
Chain Length:394
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Gene (Uniprot):GNB1
Chain IDs:B
Chain Length:345
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Soluble cytochrome b562,Prostaglandin D2 receptor
Gene (Uniprot):cybC, PTGDR
Chain IDs:C (auth: D)
Chain Length:468
Number of Molecules:1
Biological Source:Escherichia coli, Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Gene (Uniprot):GNG2
Chain IDs:D (auth: G)
Chain Length:71
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:nanobody Nb35
Chain IDs:E (auth: N)
Chain Length:156
Number of Molecules:1
Biological Source:Lama glama
Primary Citation
Molecular basis for ligand recognition and receptor activation of the prostaglandin D2 receptor DP1.
Proc.Natl.Acad.Sci.USA 122 e2501902122 e2501902122 (2025)
PMID: 40440061 DOI: 10.1073/pnas.2501902122

Abstact

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.

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