4QKX

Structure of beta2 adrenoceptor bound to a covalent agonist and an engineered nanobody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Covalent agonists for studying G protein-coupled receptor activation.

Weichert, D.Kruse, A.C.Manglik, A.Hiller, C.Zhang, C.Hubner, H.Kobilka, B.K.Gmeiner, P.

(2014) Proc.Natl.Acad.Sci.USA 111: 10744-10748

  • DOI: 10.1073/pnas.1410415111

  • PubMed Abstract: 
  • Structural studies on G protein-coupled receptors (GPCRs) provide important insights into the architecture and function of these important drug targets. However, the crystallization of GPCRs in active states is particularly challenging, requiring the ...

    Structural studies on G protein-coupled receptors (GPCRs) provide important insights into the architecture and function of these important drug targets. However, the crystallization of GPCRs in active states is particularly challenging, requiring the formation of stable and conformationally homogeneous ligand-receptor complexes. Native hormones, neurotransmitters, and synthetic agonists that bind with low affinity are ineffective at stabilizing an active state for crystallogenesis. To promote structural studies on the pharmacologically highly relevant class of aminergic GPCRs, we here present the development of covalently binding molecular tools activating Gs-, Gi-, and Gq-coupled receptors. The covalent agonists are derived from the monoamine neurotransmitters noradrenaline, dopamine, serotonin, and histamine, and they were accessed using a general and versatile synthetic strategy. We demonstrate that the tool compounds presented herein display an efficient covalent binding mode and that the respective covalent ligand-receptor complexes activate G proteins comparable to the natural neurotransmitters. A crystal structure of the β2-adrenoreceptor in complex with a covalent noradrenaline analog and a conformationally selective antibody (nanobody) verified that these agonists can be used to facilitate crystallogenesis.


    Organizational Affiliation

    Department of Chemistry and Pharmacy, Friedrich Alexander University, 91052 Erlangen, Germany; and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-2 adrenergic receptor
A
469Enterobacteria phage T4Homo sapiens
This entity is chimeric
Gene Names: E, ADRB2 (ADRB2R, B2AR)
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Find proteins for P07550 (Homo sapiens)
Go to Gene View: ADRB2
Go to UniProtKB:  P07550
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
R9 protein
B
120N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
35V
Query on 35V

Download SDF File 
Download CCD File 
A
4-[(1R)-1-hydroxy-2-({2-[3-methoxy-4-(2-sulfanylethoxy)phenyl]ethyl}amino)ethyl]benzene-1,2-diol
C19 H25 N O5 S
ABMSPPLJHILUDP-KRWDZBQOSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.558α = 90.00
b = 67.211β = 90.00
c = 301.269γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-08-20
    Type: Database references
  • Version 1.2: 2017-06-28
    Type: Database references, Source and taxonomy