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| Title | Cryo-EM structure of the DSO-5a-bound human BRS3-Gq complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Keywords | DSO-5a / MEMBRANE PROTEIN | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Function / homology | Function and homology informationbombesin receptor activity / Oplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / adult feeding behavior / neuropeptide receptor activity / negative regulation of calcium ion-dependent exocytosis / G protein-coupled adenosine receptor signaling pathway / negative regulation of adenylate cyclase activity / positive regulation of urine volume ...bombesin receptor activity / Oplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / adult feeding behavior / neuropeptide receptor activity / negative regulation of calcium ion-dependent exocytosis / G protein-coupled adenosine receptor signaling pathway / negative regulation of adenylate cyclase activity / positive regulation of urine volume / positive regulation of neural precursor cell proliferation / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / negative regulation of synaptic transmission / Vasopressin regulates renal water homeostasis via Aquaporins / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / G alpha (i) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / photoreceptor outer segment membrane / G alpha (s) signalling events / G alpha (q) signalling events / spectrin binding / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / gamma-aminobutyric acid signaling pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / alkylglycerophosphoethanolamine phosphodiesterase activity / regulation of calcium ion transport / negative regulation of apoptotic signaling pathway / PKA activation in glucagon signalling / developmental growth / hair follicle placode formation / photoreceptor outer segment / D1 dopamine receptor binding / intracellular transport / neuronal dense core vesicle / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / activation of adenylate cyclase activity / Hedgehog 'off' state / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of superoxide anion generation / adenylate cyclase-activating adrenergic receptor signaling pathway / Adenylate cyclase inhibitory pathway / cardiac muscle cell apoptotic process / photoreceptor inner segment / response to nutrient / cellular response to glucagon stimulus / regulation of insulin secretion / bioluminescence / Peptide ligand-binding receptors / hippocampal mossy fiber to CA3 synapse / adenylate cyclase activator activity / trans-Golgi network membrane / Regulation of insulin secretion / negative regulation of inflammatory response to antigenic stimulus / G protein-coupled receptor binding / bone development / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / platelet aggregation / regulation of blood pressure / cognition / G-protein beta/gamma-subunit complex binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / glucose metabolic process Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Biological species | Homo sapiens (human) / Oplophorus gracilirostris (crustacean) / ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Authors | Li J / Li C / Zhou Q / Han W / Fang M / Xu Y / Mai Y / Cui J / Xu H / Zhang Y ...Li J / Li C / Zhou Q / Han W / Fang M / Xu Y / Mai Y / Cui J / Xu H / Zhang Y / Yin W / Wang M | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Funding support | China, 17 items
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Citation | Journal: Acta Pharm Sin B / Year: 2025Title: Divergent activation patterns of BRS3 revealed by two Chinese herb-derived agonists. Authors: Jie Li / Changyao Li / Qingtong Zhou / Wei Han / Mingzhu Fang / Youwei Xu / Yiting Mai / Yao Zhang / Jiahua Cui / H Eric Xu / Yan Zhang / Wanchao Yin / Ming-Wei Wang / ![]() Abstract: Bombesin receptor subtype-3 (BRS3) is an orphan G protein-coupled receptor (GPCR) that plays critical roles in energy homeostasis, glucose metabolism, and insulin secretion. Recent structural studies ...Bombesin receptor subtype-3 (BRS3) is an orphan G protein-coupled receptor (GPCR) that plays critical roles in energy homeostasis, glucose metabolism, and insulin secretion. Recent structural studies have elucidated BRS3 signaling mechanisms using synthetic ligands, including BA1 and MK-5046. However, the molecular basis of BRS3 activation by bioactive natural compounds and their derivatives, particularly those derived from traditional Chinese medicine, remains unclear. Here, we present high-resolution cryogenic electron microscopy (cryo-EM) structures of the human BRS3-G complex in both unliganded and active states bound by two herb-derived compounds (DSO-5a and oridonin), at resolutions of 2.9, 2.8, and 2.9 Å, respectively. These structures display distinct ligand recognition patterns between DSO-5a and oridonin. Although both compounds bind to the orthosteric pocket, they differentially engage the interaction network of BRS3, as demonstrated by mutagenesis studies assessing calcium mobilization and inositol phosphate 1 (IP1) accumulation. These findings enhance our understanding of BRS3 activation and provide valuable insights into the development of small-molecule BRS3 modulators with therapeutic potential. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_61941.map.gz | 59.6 MB | EMDB map data format | |
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| Header (meta data) | emd-61941-v30.xml emd-61941.xml | 26.4 KB 26.4 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_61941_fsc.xml | 8.4 KB | Display | FSC data file |
| Images | emd_61941.png | 110.4 KB | ||
| Filedesc metadata | emd-61941.cif.gz | 7.6 KB | ||
| Others | emd_61941_half_map_1.map.gz emd_61941_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-61941 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-61941 | HTTPS FTP |
-Validation report
| Summary document | emd_61941_validation.pdf.gz | 969.4 KB | Display | EMDB validaton report |
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| Full document | emd_61941_full_validation.pdf.gz | 968.9 KB | Display | |
| Data in XML | emd_61941_validation.xml.gz | 16.5 KB | Display | |
| Data in CIF | emd_61941_validation.cif.gz | 21.5 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-61941 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-61941 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9k07MC ![]() 9lwpC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_61941.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.071 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #2
| File | emd_61941_half_map_1.map | ||||||||||||
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-Half map: #1
| File | emd_61941_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
-Entire : Cryo-EM structure of the DSO-5a-bound human BRS3-miniGq complex
| Entire | Name: Cryo-EM structure of the DSO-5a-bound human BRS3-miniGq complex |
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| Components |
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-Supramolecule #1: Cryo-EM structure of the DSO-5a-bound human BRS3-miniGq complex
| Supramolecule | Name: Cryo-EM structure of the DSO-5a-bound human BRS3-miniGq complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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| Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Bombesin receptor subtype-3,Oplophorus-luciferin 2-monooxygenase ...
| Macromolecule | Name: Bombesin receptor subtype-3,Oplophorus-luciferin 2-monooxygenase catalytic subunit type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Oplophorus-luciferin 2-monooxygenase |
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| Source (natural) | Organism: Oplophorus gracilirostris (crustacean) |
| Molecular weight | Theoretical: 67.457555 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: MKTIIALSYI FCLVFAMAQR QPHSPNQTLI SITNDTESSS SVVSNDNTNK GWSGDNSPGI EALCAIYITY AVIISVGILG NAILIKVFF KTKSMQTVPN IFITSLAFGD LLLLLTCVPV DATHYLAEGW LFGRIGCKVL SFIRLTSVGV SVFTLTILSA D RYKAVVKP ...String: MKTIIALSYI FCLVFAMAQR QPHSPNQTLI SITNDTESSS SVVSNDNTNK GWSGDNSPGI EALCAIYITY AVIISVGILG NAILIKVFF KTKSMQTVPN IFITSLAFGD LLLLLTCVPV DATHYLAEGW LFGRIGCKVL SFIRLTSVGV SVFTLTILSA D RYKAVVKP LERQPSNAIL KTCVKAGCVW IVSMIFALPE AIFSNVYTFR DPNKNMTFES CTSYPVSKKL LQEIHSLLCF LV FYIIPLS IISVYYSLIA RTLYKSTLNI PTEEQSHARK QIESRKRIAR TVLVLVALFA LCWLPNHLLY LYHSFTSQTY VDP SAMHFI FTIFSRVLAF SNSCVNPFAL YWLSKSFQKH FKAQLFCCKA ERPEPPVADT SLTTLAVMGT VPGTGSIQMS EISV TSFTG CSVKQAEDRF GSSGGGGSGG GGSSGVFTLE DFVGDWEQTA AYNLDQVLEQ GGVSSLLQNL AVSVTPIQRI VRSGE NALK IDIHVIIPYE GLSADQMAQI EEVFKVVYPV DDHHFKVILP YGTLVIDGVT PNMLNYFGRP YEGIAVFDGK KITVTG TLW NGNKIIDERL ITPDGSMLFR VTINSGGSEN LYFQGGSAGS AHHHHHHHH UniProtKB: Bombesin receptor subtype-3, Oplophorus-luciferin 2-monooxygenase catalytic subunit |
-Macromolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine n...
| Macromolecule | Name: Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short type: protein_or_peptide / ID: 2 / Details: Gi2-mini-Gq chimeric,Gi2-mini-Gq chimeric / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 28.084832 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: MGSTVSAEDK AAAERSKMID KNLREDGEKA RRTLRLLLLG ADNSGKSTIV KQMRILHGGS GGSGGTSGIF ETKFQVDKVN FHMFDVGGQ RDERRKWIQC FNDVTAIIFV VDSSDYNRLQ EALNDFKSIW NNRWLRTISV ILFLNKQDLL AEKVLAGKSK I EDYFPEFA ...String: MGSTVSAEDK AAAERSKMID KNLREDGEKA RRTLRLLLLG ADNSGKSTIV KQMRILHGGS GGSGGTSGIF ETKFQVDKVN FHMFDVGGQ RDERRKWIQC FNDVTAIIFV VDSSDYNRLQ EALNDFKSIW NNRWLRTISV ILFLNKQDLL AEKVLAGKSK I EDYFPEFA RYTTPEDATP EPGEDPRVTR AKYFIRKEFV DISTASGDGR HICYPHFTCA VDTENARRIF NDCKDIILQM NL REYNLV UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-2, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(s) subunit alpha ...UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-2, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |
-Macromolecule #3: scFv16
| Macromolecule | Name: scFv16 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: ![]() |
| Molecular weight | Theoretical: 28.668922 KDa |
| Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
| Sequence | String: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KAAALEVLFQ GPHHHHHHHH |
-Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
| Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: ![]() |
| Molecular weight | Theoretical: 37.915496 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: MGSLLQSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD ...String: MGSLLQSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD TTCALWDIET GQQTTTFTGH TGDVMSLSLA PDTRLFVSGA CDASAKLWDV REGMCRQTFT GHESDINAIC FF PNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRAGVLAGHD NRV SCLGVT DDGMAVATGS WDSFLKIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
| Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: ![]() |
| Molecular weight | Theoretical: 7.729947 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: ASNNTASIAQ ARKLVEQLKM EANIDRIKVS KAAADLMAYC EAHAKEDPLL TPVPASENPF REKKFFCAIL UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Macromolecule #6: Nanobody-35
| Macromolecule | Name: Nanobody-35 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: ![]() |
| Molecular weight | Theoretical: 15.343019 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: MAQVQLQESG GGLVQPGGSL RLSCAASGFT FSNYKMNWVR QAPGKGLEWV SDISQSGASI SYTGSVKGRF TISRDNAKNT LYLQMNSLK PEDTAVYYCA RCPAPFTRDC FDVTSTTYAY RGQGTQVTVS SHHHHHHEPE A |
-Macromolecule #7: [(1~{S})-1-[1,4-dimethoxy-8-nitroso-5-(oxidanylamino)naphthalen-2...
| Macromolecule | Name: [(1~{S})-1-[1,4-dimethoxy-8-nitroso-5-(oxidanylamino)naphthalen-2-yl]-2,2-dimethyl-but-3-enyl] furan-2-carboxylate type: ligand / ID: 7 / Number of copies: 1 / Formula: A1EL6 |
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| Molecular weight | Theoretical: 440.446 Da |
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | FEI TECNAI 10 |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
| Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
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Keywords
Homo sapiens (human)
Oplophorus gracilirostris (crustacean)
Authors
China, 17 items
Citation






























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