9UVZ | pdb_00009uvz

Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425

• PDB DOI: https://doi.org/10.2210/pdb9UVZ/pdb
• EM Map EMD-64542: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-05-11 Released: 2026-05-06 
• Deposition Author(s): Kojima, A., Kawakami, K., Kobayashi, K., Matsui, T.E., Uemoto, K., Fukuda, M., Kato, H.E.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A Rapid and Universal Pipeline for High-Resolution GPCR Structure Determination through In Silico Construct Optimization and de novo Protein Design

Kojima, A., Kawakami, K., Kobayashi, N., Kobayashi, K., Matsui, T.E., Uemoto, K., Gu, Y., Fukuda, M., Kato, H.E.

(2026) bioRxiv 

• DOI: https://doi.org/10.64898/2026.04.02.716066

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 86.66 kDa 
• Atom Count: 5,487 
• Modeled Residue Count: 682 
• Deposited Residue Count: 759 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysophosphatidic acid receptor 2,ARK1	A	759	Homo sapiens, synthetic construct	Mutation(s): 0  Gene Names: LPAR2, EDG4, LPA2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HBW0 (Homo sapiens) Explore Q9HBW0  Go to UniProtKB:  Q9HBW0
PHAROS:  Q9HBW0 GTEx:  ENSG00000064547

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L9P (Subject of Investigation/LOI)	B [auth A]	3-[[4-[4-[[(1~{R})-1-(2-chlorophenyl)ethoxy]carbonylamino]-3-methyl-1,2-oxazol-5-yl]phenyl]methylsulfanyl]propanoic acid C23 H23 Cl N2 O5 S LLIFMNUXGDHTRO-OAHLLOKOSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	REFMAC	5.8.0425

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-06 
Deposition Author(s): Kojima, A., Kawakami, K., Kobayashi, K., Matsui, T.E., Uemoto, K., Fukuda, M., Kato, H.E.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJAX222F
Japan Science and Technology	Japan	JPMJPR24OF
Japan Society for the Promotion of Science (JSPS)	Japan	25K09525
Japan Society for the Promotion of Science (JSPS)	Japan	24H02262
Japan Society for the Promotion of Science (JSPS)	Japan	25H01338
Japan Society for the Promotion of Science (JSPS)	Japan	JP24KJ0981

Revision History  

• Version 1.0: 2026-05-06
  Type: Initial release