9CM3 | pdb_00009cm3

Cryo-EM structure of Gq-coupled FFA2 in complex with TUG-1375 and compound 187


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Allosteric modulation and biased signalling at free fatty acid receptor 2.

Zhang, X.Guseinov, A.A.Jenkins, L.Valentini, A.Marsango, S.Schultz-Knudsen, K.Ulven, T.Rexen Ulven, E.Tikhonova, I.G.Milligan, G.Zhang, C.

(2025) Nature 643: 1428-1438

  • DOI: https://doi.org/10.1038/s41586-025-09186-6
  • Primary Citation of Related Structures:  
    9CLW, 9CM3, 9CM7, 9NS9

  • PubMed Abstract: 

    Free fatty acid receptor 2 (FFA2) is a G protein-coupled receptor (GPCR) that is a primary sensor for short-chain fatty acids produced by gut microbiota. Consequently, FFA2 is a promising drug target for immunometabolic disorders 1-4 . Here we report cryogenic electronic microscopy structures of FFA2 in complex with two G proteins and three distinct classes of positive allosteric modulators (PAMs), and describe noncanonical activation mechanisms that involve conserved structural features of class A GPCRs. Two PAMs disrupt the E/DRY activation microswitch 5 and stabilize the conformation of intracellular loop 2 by binding to lipid-facing pockets near the cytoplasmic side of the receptor. By contrast, the third PAM promotes the separation of transmembrane helices 6 and 7 by interacting with transmembrane helix 6 at the receptor-lipid interface. Molecular dynamic simulations and mutagenesis experiments confirm these noncanonical activation mechanisms. Furthermore, we demonstrate the molecular basis for the G i versus G q bias, which is due to distinct conformations of intracellular loop 2 stabilized by different PAMs. These findings provide a framework for the design of tailored GPCR modulators, with implications that extend beyond FFA2 to the broader field of GPCR drug discovery.


  • Organizational Affiliation
    • Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(q) subunit alpha246Homo sapiensMutation(s): 0 
Gene Names: GNAQ
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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-1376Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16C [auth N]266Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Free fatty acid receptor 2D [auth R]544Homo sapiensMutation(s): 0 
Gene Names: FFAR2FFA2GPCR43GPR43
UniProt & NIH Common Fund Data Resources
Find proteins for O15552 (Homo sapiens)
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PHAROS:  O15552
GTEx:  ENSG00000126262 
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UniProt GroupO15552
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
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Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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  • Reference Sequence
Small Molecules
Ligands 4 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
A1AZC (Subject of Investigation/LOI)
Query on A1AZC

Download Ideal Coordinates CCD File 
G [auth R]4-[(2R,6S)-2,6-dimethylmorpholin-4-yl]-7-(2-fluorobenzene-1-sulfonyl)-2-methyl-5H-pyrrolo[3,2-d]pyrimidin-6-amine
C19 H22 F N5 O3 S
FFKYPPBXLPNOOV-PHIMTYICSA-N
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
H [auth R]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
I [auth R]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM128641

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-09
    Changes: Data collection, Database references
  • Version 1.3: 2025-08-13
    Changes: Data collection, Database references