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Structure paper

TitleMolecular basis of lipid and ligand regulation of prostaglandin receptor DP2.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 121, Issue 51, Page e2403304121, Year 2024
Publish dateDec 17, 2024
AuthorsJiuyin Xu / Youwei Xu / Li Hou / Xinheng He / Yang Li / Jing Zhao / Xue Meng / James Jiqi Wang / Yanli Wu / Heng Zhang / Yunhai Li / Wen Hu / Qingning Yuan / Kai Wu / Xi Cheng / Yi Jiang / Yu Xia / H Eric Xu / Canrong Wu /
PubMed AbstractProstaglandin D2 receptor 2 (DP2) is an important anti-inflammatory and antiallergic drug target. While inactive DP2 structures are known, its activation mechanisms and biased signaling remain ...Prostaglandin D2 receptor 2 (DP2) is an important anti-inflammatory and antiallergic drug target. While inactive DP2 structures are known, its activation mechanisms and biased signaling remain unclear. Here, we report cryo-EM structures of an apo DP2-Gi complex, a DP2-Gi complex bound to the endogenous ligand Prostaglandin D (PGD), and a DP2-Gi complex bound to indomethacin, an arrestin-biased ligand, at resolutions of 2.5 Å, 2.8Å, and 2.3 Å, respectively. These structures reveal a distinct binding pose of PGD and indomethacin and provide key insights into receptor activation and transducer coupling. Combining the structural data with functional studies, we uncover the molecular basis for biased signaling of indomethacin toward β-arrestin over G proteins. Notably, a phospholipid binding site was identified at the DP2-G protein interface that modulates DP2-G protein interactions. Together, our functional and structural findings provide insights into DP2 activation, biased signaling, drug interactions, and lipid regulation, enabling rational design of safer antiallergy therapeutics targeting this key immune receptor.
External linksProc Natl Acad Sci U S A / PubMed:39665758 / PubMed Central
MethodsEM (single particle)
Resolution2.33 - 2.82 Å
Structure data

38761

8xxu

EMDB-38761, PDB-8xxu:
Cryo-EM Structure of the Prostaglandin D2 Receptor 2 Coupled to G Protein
Method: EM (single particle) / Resolution: 2.54 Å

38762

8xxv

EMDB-38762, PDB-8xxv:
Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
Method: EM (single particle) / Resolution: 2.33 Å

60994

9iyb

EMDB-60994, PDB-9iyb:
Cryo-EM Structure of the Prostaglandin D2 Receptor 2-PGD2 Coupled to G Protein
Method: EM (single particle) / Resolution: 2.82 Å

Chemicals

PDB-1d5q:
SOLUTION STRUCTURE OF A MINI-PROTEIN REPRODUCING THE CORE OF THE CD4 SURFACE INTERACTING WITH THE HIV-1 ENVELOPE GLYCOPROTEIN

ChemComp-IMN:
INDOMETHACIN / medication, antiinflammatory*YM

ChemComp-HOH:
WATER

ChemComp-PG2:
PROSTAGLANDIN D2

Source
  • homo sapiens (human)
  • mus musculus (house mouse)
  • rattus norvegicus (Norway rat)
KeywordsMEMBRANE PROTEIN / GPCR / Prostaglandin / PTGDR2 / Indomethacin / DP2 / PGD2

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