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- EMDB-66823: Cryo-EM structure of the Bavachalcone bound FFAR4-Giq complex -

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Entry
Database: EMDB / ID: EMD-66823
TitleCryo-EM structure of the Bavachalcone bound FFAR4-Giq complex
Map data
Sample
  • Complex: The Bavachalcone bound FFAR4-Giq complex
    • Protein or peptide: Free fatty acid receptor 4
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • 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
KeywordsComplex / 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 / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / GDP binding / photoreceptor disc membrane / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / glucose homeostasis / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / cilium / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of cold-induced thermogenesis / GPER1 signaling
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. / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain ...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. / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G protein beta WD-40 repeat protein / G-protein, beta subunit / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(q) subunit alpha / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / 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: 2.99 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_66823.png

Downloads & links

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Map

FileDownload / File: emd_66823.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.7257811 - 2.6632187
Average (Standard dev.)-0.001209667 (±0.052277945)
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_66823_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_66823_half_map_2.map
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Sample components

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Entire : The Bavachalcone bound FFAR4-Giq complex

EntireName: The Bavachalcone bound FFAR4-Giq complex
Components
  • Complex: The Bavachalcone bound FFAR4-Giq complex
    • Protein or peptide: Free fatty acid receptor 4
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • 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 Bavachalcone bound FFAR4-Giq complex

SupramoleculeName: The Bavachalcone bound FFAR4-Giq complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.020664 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHG SLLQSELDQL RQEAEQLKNQ IRDARKACAD ATLSQITNNI DPVGRIQMRT RRTLRGHLAK IYAMHWGTDS RLLVSASQD GKLIIWDSYT TNKVHAIPLR SSWVMTCAYA PSGNYVACGG LDNICSIYNL KTREGNVRVS RELAGHTGYL S CCRFLDDN ...String:
MHHHHHHHHG SLLQSELDQL RQEAEQLKNQ IRDARKACAD ATLSQITNNI DPVGRIQMRT RRTLRGHLAK IYAMHWGTDS RLLVSASQD GKLIIWDSYT TNKVHAIPLR SSWVMTCAYA PSGNYVACGG LDNICSIYNL KTREGNVRVS RELAGHTGYL S CCRFLDDN QIVTSSGDTT CALWDIETGQ QTTTFTGHTG DVMSLSLAPD TRLFVSGACD ASAKLWDVRE GMCRQTFTGH ES DINAICF FPNGNAFATG SDDATCRLFD LRADQELMTY SHDNIICGIT SVSFSKSGRL LLAGYDDFNC NVWDALKADR AGV LAGHDN RVSCLGVTDD GMAVATGSWD SFLKIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #4: 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: 4 / 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 #5: (~{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: 5 / 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: 2.99 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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