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 7DH5 | pdb_00007dh5

Dog beta3 adrenergic receptor bound to mirabegron in complex with a miniGs heterotrimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7DH5

This is version 1.2 of the entry. See complete history. 

Literature

Cryo-EM structure of the beta 3-adrenergic receptor reveals the molecular basis of subtype selectivity.

Nagiri, C., Kobayashi, K., Tomita, A., Kato, M., Kobayashi, K., Yamashita, K., Nishizawa, T., Inoue, A., Shihoya, W., Nureki, O.

(2021) Mol Cell 81: 3205-3215.e5

  • DOI: https://doi.org/10.1016/j.molcel.2021.06.024
  • Primary Citation Related Structures: 
    7DH5, 7XJH

  • PubMed Abstract: 

    The β 3 -adrenergic receptor (β 3 AR) is predominantly expressed in adipose tissue and urinary bladder and has emerged as an attractive drug target for the treatment of type 2 diabetes, obesity, and overactive bladder (OAB). Here, we report the cryogenic electron microscopy structure of the β 3 AR-G s signaling complex with the selective agonist mirabegron, a first-in-class drug for OAB. Comparison of this structure with the previously reported β 1 AR and β 2 AR structures reveals a receptor activation mechanism upon mirabegron binding to the orthosteric site. Notably, the narrower exosite in β 3 AR creates a perpendicular pocket for mirabegron. Mutational analyses suggest that a combination of both the exosite shape and the amino-acid-residue substitutions defines the drug selectivity of the βAR agonists. Our findings provide a molecular basis for βAR subtype selectivity, allowing the design of more-selective agents with fewer adverse effects.


  • Organizational Affiliation: 
    • Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecule Content 

  • Total Structure Weight: 133.11 kDa 
  • Atom Count: 7,850 
  • Modeled Residue Count: 1,027 
  • Deposited Residue Count: 1,200 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short249Homo sapiensMutation(s): 0 
Gene Names: GNAS, GNAS1, GSP
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
Entity Groups
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UniProt GroupP63092
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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-1351Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus)
Explore P54311 
Go to UniProtKB:  P54311
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UniProt GroupP54311
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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]68Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt
Find proteins for P63212 (Bos taurus)
Explore P63212 
Go to UniProtKB:  P63212
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UniProt GroupP63212
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
nanobody Nb35D [auth N]137unidentifiedMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-3 adrenergic receptorE [auth R]395Canis lupus familiarisMutation(s): 0 
Gene Names: ADRB3, B3AR
Membrane Entity: Yes 
UniProt
Find proteins for O02662 (Canis lupus familiaris)
Explore O02662 
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UniProt GroupO02662
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H6U
(Subject of Investigation/LOI)

Query on H6U



Download:Ideal Coordinates CCD File
F [auth R]2-(2-azanyl-1,3-thiazol-4-yl)-N-[4-[2-[[(2R)-2-oxidanyl-2-phenyl-ethyl]amino]ethyl]phenyl]ethanamide
C21 H24 N4 O2 S
PBAPPPCECJKMCM-IBGZPJMESA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan16H06294

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2021-08-18
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary