5WF5

Agonist bound human A2a adenosine receptor with D52N mutation at 2.60 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation 3D Report Full Report



Literature

Structural Connection between Activation Microswitch and Allosteric Sodium Site in GPCR Signaling.

White, K.L.Eddy, M.T.Gao, Z.G.Han, G.W.Lian, T.Deary, A.Patel, N.Jacobson, K.A.Katritch, V.Stevens, R.C.

(2018) Structure 26: 259-269.e5

  • DOI: 10.1016/j.str.2017.12.013
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Sodium ions are endogenous allosteric modulators of many G-protein-coupled receptors (GPCRs). Mutation of key residues in the sodium binding motif causes a striking effect on G-protein signaling. We report the crystal structures of agonist complexes ...

    Sodium ions are endogenous allosteric modulators of many G-protein-coupled receptors (GPCRs). Mutation of key residues in the sodium binding motif causes a striking effect on G-protein signaling. We report the crystal structures of agonist complexes for two variants in the first sodium coordination shell of the human A 2A adenosine receptor, D52 2.50 N and S91 3.39 A. Both structures present an overall active-like conformation; however, the variants show key changes in the activation motif NPxxY. Changes in the hydrogen bonding network in this microswitch suggest a possible mechanism for modified G-protein signaling and enhanced thermal stability. These structures, signaling data, and thermal stability analysis with a panel of pharmacological ligands provide a basis for understanding the role of the sodium-coordinating residues on stability and G-protein signaling. Utilizing the D 2.50 N variant is a promising method for stabilizing class A GPCRs to accelerate structural efforts and drug discovery.


    Organizational Affiliation

    Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA. Electronic address: stevens@usc.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Human A2a adenosine receptor T4L chimera
A
504Homo sapiensEscherichia virus T4Mutation(s): 5 
Gene Names: ADORA2AADORA2
EC: 3.2.1.17
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
A2A adenosine receptor with bound UK432097, D52N mutant
Find proteins for P29274 (Homo sapiens)
Go to UniProtKB:  P29274
NIH Common Fund Data Resources
PHAROS  P29274
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UKA
Query on UKA

Download CCD File 
A
6-(2,2-diphenylethylamino)-9-[(2R,3R,4S,5S)-5-(ethylcarbamoyl)-3,4-dihydroxy-oxolan-2-yl]-N-[2-[(1-pyridin-2-ylpiperidin-4-yl)carbamoylamino]ethyl]purine-2-carboxamide
C40 H47 N11 O6
ZOTHAEBAWXWVID-HXEFRTELSA-N
 Ligand Interaction
OLC
Query on OLC

Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.686α = 90
b = 77.769β = 101.05
c = 86.488γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release