8Y6W | pdb_00008y6w

TUG-1375 and 4-CMTB-bound human FFA2 in complex with Gi


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into lipid chain-length selectivity and allosteric regulation of FFA2.

Kugawa, M.Kawakami, K.Kise, R.Suomivuori, C.M.Tsujimura, M.Kobayashi, K.Kojima, A.Inoue, W.J.Fukuda, M.Matsui, T.E.Fukunaga, A.Koyanagi, J.Kim, S.Ikeda, H.Yamashita, K.Saito, K.Ishikita, H.Dror, R.O.Inoue, A.Kato, H.E.

(2025) Nat Commun 16: 2809-2809

  • DOI: https://doi.org/10.1038/s41467-025-57983-4
  • Primary Citation of Related Structures:  
    8Y6W, 8Y6Y

  • PubMed Abstract: 

    The free fatty acid receptor 2 (FFA2) is a G protein-coupled receptor (GPCR) that selectively recognizes short-chain fatty acids to regulate metabolic and immune functions. As a promising therapeutic target, FFA2 has been the focus of intensive development of synthetic ligands. However, the mechanisms by which endogenous and synthetic ligands modulate FFA2 activity remain unclear. Here, we present the structures of the human FFA2-Gi complex activated by the synthetic orthosteric agonist TUG-1375 and the positive allosteric modulator/allosteric agonist 4-CMTB, along with the structure of the inactive FFA2 bound to the antagonist GLPG0974. Structural comparisons with FFA1 and mutational studies reveal how FFA2 selects specific fatty acid chain lengths. Moreover, our structures reveal that GLPG0974 functions as an allosteric antagonist by binding adjacent to the orthosteric pocket to block agonist binding, whereas 4-CMTB binds the outer surface of transmembrane helices 6 and 7 to directly activate the receptor. Supported by computational and functional studies, these insights illuminate diverse mechanisms of ligand action, paving the way for precise GPCR-targeted drug design.


  • Organizational Affiliation
    • Research Center for Advanced Science and Technology, The University of Tokyo, Meguro, Tokyo, Japan.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
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Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1357Homo sapiensMutation(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 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-271Homo sapiensMutation(s): 0 
Gene Names: GNG2
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Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16259Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Free fatty acid receptor 2E [auth R]362Homo sapiensMutation(s): 0 
Gene Names: FFAR2FFA2GPCR43GPR43
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Find proteins for O15552 (Homo sapiens)
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PHAROS:  O15552
GTEx:  ENSG00000126262 
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UniProt GroupO15552
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9UJ (Subject of Investigation/LOI)
Query on 9UJ

Download Ideal Coordinates CCD File 
F [auth R](2R,4R)-2-(2-chlorophenyl)-3-[4-(3,5-dimethyl-1,2-oxazol-4-yl)phenyl]carbonyl-1,3-thiazolidine-4-carboxylic acid
C22 H19 Cl N2 O4 S
RZAMDGBOOPJHJQ-GHTZIAJQSA-N
A1LYC (Subject of Investigation/LOI)
Query on A1LYC

Download Ideal Coordinates CCD File 
G [auth R](2~{S})-2-(4-chlorophenyl)-3-methyl-~{N}-(1,3-thiazol-2-yl)butanamide
C14 H15 Cl N2 O S
AZYDQCGCBQYFSE-LBPRGKRZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21H05142
Japan Society for the Promotion of Science (JSPS)Japan21H04791

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references