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Yorodumi- EMDB-47802: Cryo-EM structure of the PGD2-bound prostaglandin D2 receptor (DP... -
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Basic information
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| Title | Cryo-EM structure of the PGD2-bound prostaglandin D2 receptor (DP1)-Gs complex | |||||||||
Map data | structure of the PGD2-bound prostaglandin D2 receptor (DP1)-Gs complex | |||||||||
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Keywords | GPCR / DP1 / BW245C / prostaglandin D2 receptor / prostanoid DP receptor / PGD receptor / PTGDR / Gs protein / DP1-selective agonist / PGD2 / MEMBRANE PROTEIN | |||||||||
| Function / homology | Function and homology informationprostaglandin J receptor activity / prostaglandin D receptor activity / Prostanoid ligand receptors / adenosine metabolic process / cellular response to prostaglandin D stimulus / male sex determination / sleep / mast cell degranulation / PKA activation in glucagon signalling / developmental growth ...prostaglandin J receptor activity / prostaglandin D receptor activity / Prostanoid ligand receptors / adenosine metabolic process / cellular response to prostaglandin D stimulus / male sex determination / sleep / mast cell degranulation / PKA activation in glucagon signalling / developmental growth / hair follicle placode formation / intracellular transport / D1 dopamine receptor binding / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / Hedgehog 'off' state / activation of adenylate cyclase activity / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of insulin secretion / cellular response to glucagon stimulus / adenylate cyclase activator activity / trans-Golgi network membrane / negative regulation of inflammatory response to antigenic stimulus / bone development / platelet aggregation / cognition / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / sensory perception of smell / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / cellular response to prostaglandin E stimulus / heterotrimeric G-protein complex / G alpha (12/13) signalling events / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / sensory perception of taste / positive regulation of cold-induced thermogenesis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor complex adaptor activity / positive regulation of cytosolic calcium ion concentration / retina development in camera-type eye / G protein activity / GTPase binding / Ca2+ pathway / fibroblast proliferation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Ras protein signal transduction / Extra-nuclear estrogen signaling / cell population proliferation / G protein-coupled receptor signaling pathway / inflammatory response / lysosomal membrane / GTPase activity / synapse / GTP binding / protein-containing complex binding / signal transduction / extracellular exosome / metal ion binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) / ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.68 Å | |||||||||
Authors | Davoudinasab B / Cherezov V / Han GW / KIm D | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2025Title: Structural insights into the mechanism of activation and inhibition of the prostaglandin D2 receptor 1. Authors: Behnaz Davoudinasab / Aleksey Raskovalov / Woojin Lee / Donggyun Kim / Heesoo Kim / Jordy Homing Lam / Gye Won Han / Vsevolod Katritch / Vadim Cherezov / ![]() Abstract: The prostaglandin D2 receptor 1 (DP1), a member of the prostanoid G protein-coupled receptor (GPCR) family, plays critical roles in allergic responses, sleep regulation, immune modulation, and ...The prostaglandin D2 receptor 1 (DP1), a member of the prostanoid G protein-coupled receptor (GPCR) family, plays critical roles in allergic responses, sleep regulation, immune modulation, and vasodilation. Here, we present five high-resolution cryo-electron microscopy (cryo-EM) structures of the human DP1 receptor, including an apo structure, two inactive state structures bound to two different inverse agonists developed by ONO Pharmaceutical, and two active state structures in complex with the G protein and bound to the endogenous agonist PGD2 and its selective derivative BW245C. Structural analysis, complemented by molecular dynamics simulations and site-directed mutagenesis, reveals key residues involved in ligand recognition and suggests a distinct activation mechanism for DP1, which lacks most of the conserved class A GPCR motifs. Notably, the unique residue K76 within the conserved sodium pocket acts as a major activation switch, while amphiphilic helix 8 adopts an unconventional orientation essential for receptor function. These findings offer valuable insights into the structure and function of prostanoid receptors and may facilitate the development of therapeutics targeting DP1. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_47802.map.gz | 92 MB | EMDB map data format | |
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| Header (meta data) | emd-47802-v30.xml emd-47802.xml | 26.5 KB 26.5 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_47802_fsc.xml | 11.9 KB | Display | FSC data file |
| Images | emd_47802.png | 51.4 KB | ||
| Filedesc metadata | emd-47802.cif.gz | 7.6 KB | ||
| Others | emd_47802_half_map_1.map.gz emd_47802_half_map_2.map.gz | 164.9 MB 164.9 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-47802 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-47802 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9e9sMC ![]() 9au0C ![]() 9ee5C ![]() 9ei5C ![]() 9ekhC ![]() 71658 ![]() 76159 ![]() 76160 M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_47802.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | structure of the PGD2-bound prostaglandin D2 receptor (DP1)-Gs complex | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: Half Map B
| File | emd_47802_half_map_1.map | ||||||||||||
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| Annotation | Half Map B | ||||||||||||
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| Density Histograms |
-Half map: Half Map A
| File | emd_47802_half_map_2.map | ||||||||||||
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| Annotation | Half Map A | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : PGD2-bound prostaglandin D2 receptor (DP1)-Gs protein-Nb35 complex
+Supramolecule #1: PGD2-bound prostaglandin D2 receptor (DP1)-Gs protein-Nb35 complex
+Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
+Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Macromolecule #4: Prostaglandin D2 receptor
+Macromolecule #5: Nanobody35
+Macromolecule #6: PROSTAGLANDIN D2
+Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #8: CHOLESTEROL HEMISUCCINATE
+Macromolecule #9: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
United States, 1 items
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Processing
FIELD EMISSION GUN


