2Y00 | pdb_00002y00

TURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND BOUND PARTIAL AGONIST DOBUTAMINE (CRYSTAL DOB92)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.256 (Depositor) 
  • R-Value Work: 
    0.226 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history

Literature

The Structural Basis for Agonist and Partial Agonist Action on a Beta1-Adrenergic Receptor

Warne, A.Moukhametzianov, R.Baker, J.G.Nehme, R.Edwards, P.C.Leslie, A.G.W.Schertler, G.F.X.Tate, C.G.

(2011) Nature 469: 241

  • DOI: https://doi.org/10.1038/nature09746
  • Primary Citation Related Structures: 
    2Y00, 2Y01, 2Y02, 2Y03, 2Y04

  • PubMed Abstract: 

    β-adrenergic receptors (βARs) are G-protein-coupled receptors (GPCRs) that activate intracellular G proteins upon binding catecholamine agonist ligands such as adrenaline and noradrenaline. Synthetic ligands have been developed that either activate or inhibit βARs for the treatment of asthma, hypertension or cardiac dysfunction. These ligands are classified as either full agonists, partial agonists or antagonists, depending on whether the cellular response is similar to that of the native ligand, reduced or inhibited, respectively. However, the structural basis for these different ligand efficacies is unknown. Here we present four crystal structures of the thermostabilized turkey (Meleagris gallopavo) β(1)-adrenergic receptor (β(1)AR-m23) bound to the full agonists carmoterol and isoprenaline and the partial agonists salbutamol and dobutamine. In each case, agonist binding induces a 1 Å contraction of the catecholamine-binding pocket relative to the antagonist bound receptor. Full agonists can form hydrogen bonds with two conserved serine residues in transmembrane helix 5 (Ser(5.42) and Ser(5.46)), but partial agonists only interact with Ser(5.42) (superscripts refer to Ballesteros-Weinstein numbering). The structures provide an understanding of the pharmacological differences between different ligand classes, illuminating how GPCRs function and providing a solid foundation for the structure-based design of novel ligands with predictable efficacies.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

Macromolecule Content 

  • Total Structure Weight: 78.25 kDa 
  • Atom Count: 5,052 
  • Modeled Residue Count: 584 
  • Deposited Residue Count: 630 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-1 ADRENERGIC RECEPTOR
A, B
315Meleagris gallopavoMutation(s): 8 
Membrane Entity: Yes 
UniProt
Find proteins for P07700 (Meleagris gallopavo)
Explore P07700 
Go to UniProtKB:  P07700
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07700
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01

Query on Y01



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
L [auth B],
M [auth B]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
2CV

Query on 2CV



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
HEGA-10
C18 H37 N O7
ITEIKACYSCODFV-ATLSCFEFSA-N
Y00

Query on Y00



Download:Ideal Coordinates CCD File
J [auth A],
S [auth B]
DOBUTAMINE
C18 H23 N O3
JRWZLRBJNMZMFE-CYBMUJFWSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
K [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.256 (Depositor) 
  • R-Value Work:  0.226 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90α = 90
b = 60.5β = 110.2
c = 101.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-04-03
    Changes: Data collection, Experimental preparation, Other, Source and taxonomy
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.6: 2024-11-20
    Changes: Structure summary