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- PDB-9xfj: Cryo-EM structure of the Bavachalcone bound GPR120-Giq complex (l... -

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Basic information

Entry
Database: PDB / ID: 9xfj
TitleCryo-EM structure of the Bavachalcone bound GPR120-Giq complex (local refinement)
Components
  • Free fatty acid receptor 4
  • Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha
KeywordsMEMBRANE PROTEIN / FFAR4 / Agonist
Function / homology
Function and homology information


negative regulation of somatostatin secretion / positive regulation of glucagon secretion / ghrelin secretion / regulation of D-glucose transmembrane transport / Free fatty acid receptors / positive regulation of gonadotropin secretion / hormone secretion / phospholipase C-activating tachykinin receptor signaling pathway / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion ...negative regulation of somatostatin secretion / positive regulation of glucagon secretion / ghrelin secretion / regulation of D-glucose transmembrane transport / Free fatty acid receptors / positive regulation of gonadotropin secretion / hormone secretion / phospholipase C-activating tachykinin receptor signaling pathway / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / taste receptor activity / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / regulation of platelet activation / PLC beta mediated events / phospholipase C-activating serotonin receptor signaling pathway / entrainment of circadian clock / sensory perception of itch / positive regulation of membrane depolarization / phototransduction, visible light / arrestin family protein binding / negative regulation of cytokine production / regulation of canonical Wnt signaling pathway / white fat cell differentiation / negative regulation of interleukin-1 beta production / ciliary membrane / glutamate receptor signaling pathway / positive regulation of osteoblast differentiation / brown fat cell differentiation / positive regulation of brown fat cell differentiation / postsynaptic cytosol / endocytic vesicle / photoreceptor outer segment / hormone-mediated signaling pathway / cellular response to acidic pH / regulation of eating behavior / adenylate cyclase inhibitor activity / T cell migration / positive regulation of protein localization to cell cortex / positive regulation of relaxation of smooth muscle / Adenylate cyclase inhibitory pathway / D2 dopamine receptor binding / adenylate cyclase-inhibiting dopamine receptor signaling pathway / GTPase activator activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / G protein-coupled serotonin receptor binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / regulation of G protein-coupled receptor signaling pathway / fatty acid binding / cellular response to forskolin / regulation of mitotic spindle organization / mast cell degranulation / chemokine-mediated signaling pathway / establishment of mitotic spindle orientation / neuropeptide signaling pathway / Regulation of insulin secretion / response to prostaglandin E / negative regulation of inflammatory response / positive regulation of cholesterol biosynthetic process / G protein-coupled receptor binding / response to peptide hormone / blood coagulation / G protein-coupled receptor activity / G-protein beta/gamma-subunit complex binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G protein-coupled acetylcholine receptor signaling pathway / Thromboxane signalling through TP receptor / G-protein activation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / GDP binding / ADP signalling through P2Y purinoceptor 12 / glucose homeostasis / cilium / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of cold-induced thermogenesis / GPER1 signaling / heterotrimeric G-protein complex / nuclear membrane / positive regulation of cytosolic calcium ion concentration / Thrombin signalling through proteinase activated receptors (PARs) / adenylate cyclase-activating G protein-coupled receptor signaling pathway / spindle pole / ciliary basal body / cytoplasmic side of plasma membrane / midbody / G protein activity / cell cortex / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / positive regulation of ERK1 and ERK2 cascade / Extra-nuclear estrogen signaling / endosome membrane
Similarity search - Function
G-protein alpha subunit, group Q / G-protein alpha subunit, group I / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM ...G-protein alpha subunit, group Q / G-protein alpha subunit, group I / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Guanine nucleotide-binding protein G(q) subunit alpha / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Free fatty acid receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsZhu, S. / Wang, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Gα activation of free fatty acid receptor 4 suppresses metabolic dysfunction by disrupting Nr1h3-PPARγ axis.
Authors: Yulin Kong / Jixia Wang / Zhen Wang / Shuting Yang / Xianlong Ye / Wei Wang / Hui Wang / Wanjun Deng / Yanfang Liu / Fangfang Xu / Tao Hou / Yaopeng Zhao / Binyu Zhang / Xuekui Yu / Yongquan ...Authors: Yulin Kong / Jixia Wang / Zhen Wang / Shuting Yang / Xianlong Ye / Wei Wang / Hui Wang / Wanjun Deng / Yanfang Liu / Fangfang Xu / Tao Hou / Yaopeng Zhao / Binyu Zhang / Xuekui Yu / Yongquan Chen / Xinmiao Liang / Shenglong Zhu /
Abstract: Maintenance of glucose and lipid homeostasis is essential for metabolic health, and its dysregulation, driven by complex gene-environment interactions-underlies various metabolic disorders. Free ...Maintenance of glucose and lipid homeostasis is essential for metabolic health, and its dysregulation, driven by complex gene-environment interactions-underlies various metabolic disorders. Free fatty acid receptor 4 (FFAR4) has been proposed to link dietary signals with genetic metabolic predisposition, yet the precise mechanisms underlying the pathophysiological function of FFAR4 remain elusive and lack of the highly selective FFAR4 agonists. Our study shed light on the pivotal role of FFAR4 in metabolic homeostasis within metabolic organs. Hepatic FFAR4 deficiency in mice exacerbates lipid accumulation and promoted severe steatosis, whereas its overexpression ameliorates diet-induced metabolic dysfunction. Mechanistically, suppression of hepatic FFAR4 promotes lipogenesis by enhancing co-activation of the nuclear receptor Nr1h3 and PPARγ. Furthermore, we identify bavachalcone, a non-carboxylated compound isolated from the traditional Chinese medicine Psoralea corylifolia L., as a functionally effective FFAR4 agonist, which could robustly attenuate metabolic dysfunction. Structural analysis using cryo-electron microscopy reveals the binding mode of bavachalcone within the FFAR4-Gα complex and illuminated the underlying mechanisms. In conclusion, our findings highlight an indispensable role of hepatic FFAR4 in counteracting metabolic dysregulation and identify bavachalcone as a selective and translatable FFAR4 agonist worthy of further clinical evaluation.
History
DepositionOct 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Free fatty acid receptor 4
B: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4133
Polymers81,0882
Non-polymers3241
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Free fatty acid receptor 4 / G-protein coupled receptor 120 / G-protein coupled receptor 129 / G-protein coupled receptor GT01 / ...G-protein coupled receptor 120 / G-protein coupled receptor 129 / G-protein coupled receptor GT01 / G-protein coupled receptor PGR4 / Omega-3 fatty acid receptor 1


Mass: 40533.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FFAR4, GPR120, GPR129, O3FAR1, PGR4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5NUL3
#2: Protein Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha / Adenylate cyclase-inhibiting G alpha protein / Guanine nucleotide-binding protein alpha-q


Mass: 40555.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Gi-Gq chimera / Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1, GNAQ, GAQ / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P63096, UniProt: P50148, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#3: Chemical ChemComp-A1EZZ / (~{E})-3-(4-hydroxyphenyl)-1-[5-(3-methylbut-2-enyl)-2,4-bis(oxidanyl)phenyl]prop-2-en-1-one / Bavachalcone


Mass: 324.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The complex of Bavachalcone-FFAR4-Giq / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 186477 / Symmetry type: POINT

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