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- EMDB-66824: Cryo-EM structure of the Bavachalcone bound GPR120-Giq complex (l... -

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Basic information

Entry
Database: EMDB / ID: EMD-66824
TitleCryo-EM structure of the Bavachalcone bound GPR120-Giq complex (local refinement)
Map data
Sample
  • Complex: The complex of Bavachalcone-FFAR4-Giq
    • Protein or peptide: Free fatty acid receptor 4
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha
  • Ligand: (~{E})-3-(4-hydroxyphenyl)-1-[5-(3-methylbut-2-enyl)-2,4-bis(oxidanyl)phenyl]prop-2-en-1-one
KeywordsFFAR4 / Agonist / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsZhu S / Wang Z
Funding support1 items
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, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66824.png

Downloads & links

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Map

FileDownload / File: emd_66824.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.616 Å		1.06 Å/pix.
x 256 pix.
= 271.616 Å		1.06 Å/pix.
x 256 pix.
= 271.616 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.7062955 - 2.5438988
Average (Standard dev.)-0.0012448404 (±0.035845265)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66824_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_66824_half_map_2.map
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Sample components

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Entire : The complex of Bavachalcone-FFAR4-Giq

EntireName: The complex of Bavachalcone-FFAR4-Giq
Components
  • Complex: The complex of Bavachalcone-FFAR4-Giq
    • Protein or peptide: Free fatty acid receptor 4
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha
  • Ligand: (~{E})-3-(4-hydroxyphenyl)-1-[5-(3-methylbut-2-enyl)-2,4-bis(oxidanyl)phenyl]prop-2-en-1-one

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Supramolecule #1: The complex of Bavachalcone-FFAR4-Giq

SupramoleculeName: The complex of Bavachalcone-FFAR4-Giq / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Free fatty acid receptor 4

MacromoleculeName: Free fatty acid receptor 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.533211 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSPECARAAG DAPLRSLEQA NRTRFPFFSD VKGDHRLVLA AVETTVLVLI FAVSLLGNVC ALVLVARRRR RGATACLVLN LFCADLLFI SAIPLVLAVR WTEAWLLGPV ACHLLFYVMT LSGSVTILTL AAVSLERMVC IVHLQRGVRG PGRRARAVLL A LIWGYSAV ...String:
MSPECARAAG DAPLRSLEQA NRTRFPFFSD VKGDHRLVLA AVETTVLVLI FAVSLLGNVC ALVLVARRRR RGATACLVLN LFCADLLFI SAIPLVLAVR WTEAWLLGPV ACHLLFYVMT LSGSVTILTL AAVSLERMVC IVHLQRGVRG PGRRARAVLL A LIWGYSAV AALPLCVFFR VVPQRLPGAD QEISICTLIW PTIPGEISWD VSFVTLNFLV PGLVIVISYS KILQITKASR KR LTVSLAY SESHQIRVSQ QDFRLFRTLF LLMVSFFIMW SPIIITILLI LIQNFKQDLV IWPSLFFWVV AFTFANSALN PIL YNMTLC RNEWKKIFCC FWFPEKGAIL TDTSVKRNDL SIISG

UniProtKB: Free fatty acid receptor 4

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Macromolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine n...

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha
type: protein_or_peptide / ID: 2 / Details: Gi-Gq chimera / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.555199 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGAQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHESM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCS TDTENIRFVF AAVKDTILQL NLKEYNLV

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(q) subunit alpha

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Macromolecule #3: (~{E})-3-(4-hydroxyphenyl)-1-[5-(3-methylbut-2-enyl)-2,4-bis(oxid...

MacromoleculeName: (~{E})-3-(4-hydroxyphenyl)-1-[5-(3-methylbut-2-enyl)-2,4-bis(oxidanyl)phenyl]prop-2-en-1-one
type: ligand / ID: 3 / Number of copies: 1 / Formula: A1EZZ
Molecular weightTheoretical: 324.37 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 186477
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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