9E9S | pdb_00009e9s

Cryo-EM structure of the PGD2-bound prostaglandin D2 receptor (DP1)-Gs complex

• PDB DOI: https://doi.org/10.2210/pdb9E9S/pdb
• EM Map EMD-47802: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Lama glama
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2024-11-08 Released: 2025-09-03 
• Deposition Author(s): Davoudinasab, B., Cherezov, V., Han, G.W., KIm, D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.68 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of inactive and active prostaglandin D2 receptor

Davoudinasab, B., Han, G.W., Cherezov, V.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 150.9 kDa 
• Atom Count: 8,551 
• Modeled Residue Count: 1,071 
• Deposited Residue Count: 1,334 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	394	Homo sapiens	Mutation(s): 8  Gene Names: GNAS, GNAS1, GSP EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens) Explore P63092  Go to UniProtKB:  P63092
PHAROS:  P63092 GTEx:  ENSG00000087460

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	345	Homo sapiens	Mutation(s): 0  Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873  Go to UniProtKB:  P62873
PHAROS:  P62873 GTEx:  ENSG00000078369

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin D2 receptor	D	385	Homo sapiens	Mutation(s): 0  Gene Names: PTGDR 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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q13258-1

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody35|Lama glama	E [auth N]	139	Lama glama	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y01	H [auth D]	CHOLESTEROL HEMISUCCINATE C31 H50 O4 WLNARFZDISHUGS-MIXBDBMTSA-N
PG2 (Subject of Investigation/LOI)	F [auth D]	PROSTAGLANDIN D2 C20 H32 O5 BHMBVRSPMRCCGG-OUTUXVNYSA-N
NAG	G [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.68 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Davoudinasab, B., Cherezov, V., Han, G.W., KIm, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM127086

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release