7XKA

Structure of human beta2 adrenergic receptor bound to constrained epinephrine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.231 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Constrained catecholamines gain beta 2 AR selectivity through allosteric effects on pocket dynamics.

Xu, X.Shonberg, J.Kaindl, J.Clark, M.J.Stossel, A.Maul, L.Mayer, D.Hubner, H.Hirata, K.Venkatakrishnan, A.J.Dror, R.O.Kobilka, B.K.Sunahara, R.K.Liu, X.Gmeiner, P.

(2023) Nat Commun 14: 2138-2138

  • DOI: https://doi.org/10.1038/s41467-023-37808-y
  • Primary Citation of Related Structures:  
    7XK9, 7XKA

  • PubMed Abstract: 

    G protein-coupled receptors (GPCRs) within the same subfamily often share high homology in their orthosteric pocket and therefore pose challenges to drug development. The amino acids that form the orthosteric binding pocket for epinephrine and norepinephrine in the β 1 and β 2 adrenergic receptors (β 1 AR and β 2 AR) are identical. Here, to examine the effect of conformational restriction on ligand binding kinetics, we synthesized a constrained form of epinephrine. Surprisingly, the constrained epinephrine exhibits over 100-fold selectivity for the β 2 AR over the β 1 AR. We provide evidence that the selectivity may be due to reduced ligand flexibility that enhances the association rate for the β 2 AR, as well as a less stable binding pocket for constrained epinephrine in the β 1 AR. The differences in the amino acid sequence of the extracellular vestibule of the β 1 AR allosterically alter the shape and stability of the binding pocket, resulting in a marked difference in affinity compared to the β 2 AR. These studies suggest that for receptors containing identical binding pocket residues, the binding selectivity may be influenced in an allosteric manner by surrounding residues, like those of the extracellular loops (ECLs) that form the vestibule. Exploiting these allosteric influences may facilitate the development of more subtype-selective ligands for GPCRs.


  • Organizational Affiliation

    State Key laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endolysin,Beta-2 adrenergic receptor469Tequatrovirus T4Homo sapiensMutation(s): 8 
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07550 (Homo sapiens)
Explore P07550 
Go to UniProtKB:  P07550
PHAROS:  P07550
GTEx:  ENSG00000169252 
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P07550
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Camelid Antibody Fragment120Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.6α = 90
b = 66.56β = 90
c = 302.72γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-29
    Changes: Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary