7XJI

Solabegron-activated dog beta3 adrenergic receptor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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

Cryo-EM structures of the beta 3 adrenergic receptor bound to solabegron and isoproterenol.

Nureki, I.Kobayashi, K.Tanaka, T.Demura, K.Inoue, A.Shihoya, W.Nureki, O.

(2022) Biochem Biophys Res Commun 611: 158-164

  • DOI: https://doi.org/10.1016/j.bbrc.2022.04.065
  • Primary Citation of Related Structures:  
    7XJI

  • PubMed Abstract: 

    The β 3 -adrenergic receptor (β 3 AR) is the most essential drug target for overactive bladder and has therapeutic potentials for the treatments of type 2 diabetes and obesity. Here, we report the cryo-electron microscopy structures of the β 3 AR-G s signaling complexes with the selective agonist, solabegron and the nonselective agonist, isoproterenol. Comparison of the isoproterenol-, mirabegron-, and solabegron-bound β 3 AR structures revealed that the extracellular loop 2 changes its conformation depending on the bound agonist and plays an essential role in solabegron binding. Moreover, β 3 AR has an intrinsically narrow exosite, regardless of the agonist type. This structural feature clearly explains why β 3 AR prefers mirabegron and solabegron, as the narrow exosite is suitable for binding with agonists with elongated shapes. Our study deepens the understanding of the binding characteristics of β 3 AR agonists and may pave the way for developing β 3 AR-selective drugs.


  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short380Homo sapiensMutation(s): 7 
Gene Names: GNASGNAS1GSP
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
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Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupP63092
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1351Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus)
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UniProt GroupP54311
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody-35C [auth N]137unidentifiedMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-3 adrenergic receptorD [auth R]395Canis lupus familiarisMutation(s): 0 
Gene Names: ADRB3B3AR
Membrane Entity: Yes 
UniProt
Find proteins for O02662 (Canis lupus familiaris)
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UniProt GroupO02662
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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]68Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt
Find proteins for P63212 (Bos taurus)
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UniProt GroupP63212
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EI5 (Subject of Investigation/LOI)
Query on EI5

Download Ideal Coordinates CCD File 
F [auth R]3-[3-[2-[[(2~{S})-2-(3-chlorophenyl)-2-oxidanyl-ethyl]amino]ethylamino]phenyl]benzoic acid
C23 H23 Cl N2 O3
LLDXOPKUNJTIRF-JOCHJYFZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21H05037

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references