9K07 | pdb_00009k07

Cryo-EM structure of the DSO-5a-bound human BRS3-Gq complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Divergent activation patterns of BRS3 revealed by two Chinese herb-derived agonists.

Li, J.Li, C.Zhou, Q.Han, W.Fang, M.Xu, Y.Mai, Y.Zhang, Y.Cui, J.Xu, H.E.Zhang, Y.Yin, W.Wang, M.W.

(2025) Acta Pharm Sin B 15: 5231-5243

  • DOI: https://doi.org/10.1016/j.apsb.2025.06.025
  • Primary Citation of Related Structures:  
    9K07, 9LWP

  • PubMed 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 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 q 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.


  • Organizational Affiliation
    • Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bombesin receptor subtype-3,Oplophorus-luciferin 2-monooxygenase catalytic subunitA [auth R]612Homo sapiensOplophorus gracilirostris
This entity is chimeric
Mutation(s): 0 
Gene Names: BRS3
EC: 1.13.12.13
UniProt & NIH Common Fund Data Resources
Find proteins for P32247 (Homo sapiens)
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Go to UniProtKB:  P32247
PHAROS:  P32247
GTEx:  ENSG00000102239 
Find proteins for Q9GV45 (Oplophorus gracilirostris)
Explore Q9GV45 
Go to UniProtKB:  Q9GV45
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UniProt GroupsQ9GV45P32247
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortB [auth A]246Homo sapiensMutation(s): 0 
Gene Names: GNAI2GNAI2BGNASGNAS1GSP
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P04899 (Homo sapiens)
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Go to UniProtKB:  P04899
PHAROS:  P04899
GTEx:  ENSG00000114353 
Find proteins for P63092 (Homo sapiens)
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Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupsP63092P04899
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16C [auth E]267Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1D [auth B]345Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
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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]70Bos taurusMutation(s): 0 
Gene Names: GNG2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody-35F [auth N]140Lama glamaMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EL6 (Subject of Investigation/LOI)
Query on A1EL6

Download Ideal Coordinates CCD File 
G [auth R][(1~{S})-1-[1,4-dimethoxy-8-nitroso-5-(oxidanylamino)naphthalen-2-yl]-2,2-dimethyl-but-3-enyl] furan-2-carboxylate
C23 H24 N2 O7
WUXGQZUWKGBOKK-OAQYLSRUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 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 Natural Science Foundation of China (NSFC)China82273961
National Natural Science Foundation of China (NSFC)China82073904
National Natural Science Foundation of China (NSFC)China81872915
National Natural Science Foundation of China (NSFC)China32171189
National Natural Science Foundation of China (NSFC)China32130022
National Natural Science Foundation of China (NSFC)China82121005
Other governmentChina2022YFA1302900
Other governmentChina2022YFC2703105
Other governmentChina2021278
Other governmentChinaCXTD2023010
Other governmentChina2019B090904008
Other governmentChina2021B0909050003
Other governmentChinaXDB37030103
Other governmentChina2019SHZDZX02
Other governmentChinaLG-GG-202204-01
Other governmentChina2021ZD0203400
Other governmentChinaZDKJ2021028

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Data collection, Database references