9EKH | pdb_00009ekh

Cryo-EM structure ONO3030297-bound prostaglandin D2 receptor (DP1)-bRIL-Fab complex

• PDB DOI: https://doi.org/10.2210/pdb9EKH/pdb
• EM Map EMD-48122: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-12-02 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: 2.89 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into mechanism of activation and deactivation of prostaglandin receptors

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 117.5 kDa 
• Atom Count: 7,546 
• Modeled Residue Count: 974 
• Deposited Residue Count: 1,061 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin D2 receptor,Soluble cytochrome b562	A	495	Homo sapiens	Mutation(s): 6  Gene Names: PTGDR, cybC
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for Q13258 (Homo sapiens) Explore Q13258  Go to UniProtKB:  Q13258
PHAROS:  Q13258 GTEx:  ENSG00000168229
UniProt Groups	Q13258P0ABE7
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q13258-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-BRIL Fab Heavy Chain	B [auth H]	229	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-Fab Nanobody	C [auth K]	123	synthetic construct	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-BRIL Fab Light Chain	D [auth L]	214	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BI8 (Subject of Investigation/LOI)	F [auth A]	1-[2-chloro-5-(2,6-dimethyl-4-{[(2S)-4-methyl-3,4-dihydro-2H-1,4-benzoxazin-2-yl]methoxy}benzamido)phenyl]cyclopropane-1-carboxylic acid C29 H29 Cl N2 O5 SFYMNHDVJCEATP-NRFANRHFSA-N
NAG	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.89 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