8Y52 | pdb_00008y52

Cryo-EM structure of the BA1-bound BRS3-Gq complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8Y52

This is version 1.2 of the entry. See complete history

Literature

Structural insights into ligand recognition, selectivity, and activation of bombesin receptor subtype-3.

Li, C.Xu, Y.Su, W.He, X.Li, J.Li, X.Xu, H.E.Yin, W.

(2024) Cell Rep 43: 114511-114511

  • DOI: https://doi.org/10.1016/j.celrep.2024.114511
  • Primary Citation Related Structures: 
    8Y52, 8Y53

  • PubMed Abstract: 

    Bombesin receptor subtype-3 (BRS3) is an important orphan G protein-coupled receptor that regulates energy homeostasis and insulin secretion. As a member of the bombesin receptor (BnR) family, the lack of known endogenous ligands and high-resolution structure has hindered the understanding of BRS3 signaling and function. We present two cryogenic electron microscopy (cryo-EM) structures of BRS3 in complex with the heterotrimeric G q protein in its active states: one bound to the pan-BnR agonist BA1 and the other bound to the synthetic BRS3-specific agonist MK-5046. These structures reveal the architecture of the orthosteric ligand pocket underpinning molecular recognition and provide insights into the structural basis for BRS3's selectivity and low affinity for bombesin peptides. Examination of conserved micro-switches suggests a shared activation mechanism among BnRs. Our findings shed light on BRS3's ligand selectivity and signaling mechanisms, paving the way for exploring its therapeutic potential for diabetes, obesity, and related metabolic disorders.


  • Organizational Affiliation
    • State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Lingang Laboratory, Shanghai 200031, China.

Macromolecule Content 

  • Total Structure Weight: 129.14 kDa 
  • Atom Count: 7,380 
  • Modeled Residue Count: 932 
  • Deposited Residue Count: 1,147 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(q) subunit alpha361Homo sapiensMutation(s): 0 
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P50148 (Homo sapiens)
Explore P50148 
Go to UniProtKB:  P50148
PHAROS:  P50148
GTEx:  ENSG00000156052 
Entity Groups
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UniProt GroupP50148
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1345Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
Entity Groups
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UniProt GroupP62873
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
Entity Groups
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UniProt GroupP59768
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Bombesin receptor subtype-3D [auth R]361Homo sapiensMutation(s): 0 
Gene Names: BRS3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P32247 (Homo sapiens)
Explore P32247 
Go to UniProtKB:  P32247
PHAROS:  P32247
GTEx:  ENSG00000102239 
Entity Groups
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UniProt GroupP32247
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
BA1E [auth X]9Homo sapiensMutation(s): 0 

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
BAL
Query on BAL
E [auth X]PEPTIDE-LIKEC3 H7 N O2

--

DPN
Query on DPN
E [auth X]D-PEPTIDE LINKINGC9 H11 N O2

--

NLE
Query on NLE
E [auth X]L-PEPTIDE LINKINGC6 H13 N O2LEU

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81902085

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-07-23
    Changes: Data collection