4QKX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.240 

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 U S A 111: 10744-10748

  • DOI: 10.1073/pnas.1410415111
  • Primary Citation of Related Structures:  
    4QKX

  • 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 kobilka@stanford.edu peter.gmeiner@fau.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2 adrenergic receptorA469Escherichia virus T4Homo sapiens
This entity is chimeric
Mutation(s): 7 
Gene Names: ET4Tp126
EC: 3.2.1.17
Find proteins for P07550 (Homo sapiens)
Explore P07550 
Go to UniProtKB:  P07550
NIH Common Fund Data Resources
PHAROS  P07550
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
R9 proteinB120Lama glamaMutation(s): 0 
Gene Names: r9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
35V
Query on 35V

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.558α = 90
b = 67.211β = 90
c = 301.269γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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