21TY | pdb_000021ty

Cryo-EM structure of Free fatty acid receptor 2 (FFA2)-ARK1 with GLPG0974

• PDB DOI: https://doi.org/10.2210/pdb21TY/pdb
• EM Map EMD-67995: EMDB EMDataResource

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


• Deposited: 2025-12-26 Released: 2026-09-09 
• Deposition Author(s): Kojima, A., Kawakami, K., Narita, T., Kugawa, M., Hayashi, 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: 2.93 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Universal pipeline for high-resolution GPCR structure determination.

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

(2026) Nat Struct Mol Biol 

• PubMed: 42665663 
• DOI: https://doi.org/10.1038/s41594-026-01869-6
• Primary Citation Related Structures: 
  21TY


• PubMed Abstract: 
  

  G protein-coupled receptors (GPCRs) regulate human physiology and are major drug targets. Although cryo-electron microscopy has accelerated GPCR structural biology, inactive-state structures remain difficult because current fusion-based strategies often require extensive experimental screening to identify rigid constructs suitable for high-resolution reconstruction. Here we introduce a universal pipeline that integrates an in silico fusion construct screening program, NOAH (nonexperimental, artificial-intelligence-assisted, high-throughput construct screening for structural analysis), with a de novo designed fusion protein, ARK1 (artificially designed fiducial marker). NOAH enabled structure determination of vasopressin V2 receptor bound to the antagonist tolvaptan or partial agonist OPC51803 and bradykinin B2 receptor bound to the antagonist icatibant, revealing receptor activation and inhibition mechanisms. Coupling NOAH to ARK1 improved the V2 receptor-tolvaptan map and enabled high-resolution structures of lysophosphatidic acid receptor 2 bound to Ki16425 and free fatty acid receptor 2 bound to GLPG0974. NOAH-ARK1 minimizes trial-and-error construct optimization and provides a broadly applicable route for GPCR structural analysis and drug discovery.

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Organizational Affiliation: 
• Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
Department of Life Sciences, School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
Graduate School of Pharmaceutical Sciences, Tohoku University, Miyagi, Japan.
Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
PRESTO, Japan Science and Technology Agency, Saitama, Japan.
Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan. [e-mail].
Department of Life Sciences, School of Arts and Sciences, The University of Tokyo, Tokyo, Japan. [e-mail].
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. [e-mail].
FOREST, Japan Science and Technology Agency, Saitama, Japan. [e-mail].
CREST, Japan Science and Technology Agency, Saitama, Japan. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 86.05 kDa 
• Atom Count: 5,388 
• Modeled Residue Count: 662 
• Deposited Residue Count: 748 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Free fatty acid receptor 2,human free fatty acid receptor 2 (FFA2) fused with de novo designed ARK1	A	748	Homo sapiens	Mutation(s): 0  Gene Names: FFAR2, FFA2, GPCR43, GPR43
UniProt & NIH Common Fund Data Resources
Find proteins for O15552 (Homo sapiens) Explore O15552  Go to UniProtKB:  O15552
PHAROS:  O15552 GTEx:  ENSG00000126262

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1LYD (Subject of Investigation/LOI)	B [auth A]	GLPG-0974 C25 H25 Cl N2 O4 S MPMKMQHJHDHPBE-RUZDIDTESA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.93 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	REFMAC	5.8.0425

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-09 
Deposition Author(s): Kojima, A., Kawakami, K., Narita, T., Kugawa, M., Hayashi, 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: 2026-09-09
  Type: Initial release