8Y53 | pdb_00008y53

Cryo-EM structure of the MK-5046-bound BRS3-Gq complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8Y53

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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: 170.84 kDa 
  • Atom Count: 10,071 
  • Modeled Residue Count: 1,281 
  • Deposited Residue Count: 1,535 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(q) subunit alpha361Homo sapiensMutation(s): 0 
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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
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62873
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv16C [auth E]247Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
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
Sequence Annotations
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
nanobody Nb35E [auth N]150Lama glamaMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Bombesin receptor subtype-3F [auth R]361Homo sapiensMutation(s): 0 
Gene Names: BRS3
UniProt & NIH Common Fund Data Resources
Find proteins for P32247 (Homo sapiens)
Explore P32247 
Go to UniProtKB:  P32247
PHAROS:  P32247
GTEx:  ENSG00000102239 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32247
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1D54
(Subject of Investigation/LOI)

Query on A1D54



Download:Ideal Coordinates CCD File
G [auth R](2~{S})-1,1,1-tris(fluoranyl)-2-(4-pyrazol-1-ylphenyl)-3-[5-[[1-(trifluoromethyl)cyclopropyl]methyl]-1~{H}-imidazol-2-yl]propan-2-ol
C20 H18 F6 N4 O
UJINBEQCDMOAHM-SFHVURJKSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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