2ANJ

Crystal Structure of the Glur2 Ligand Binding Core (S1S2J-Y450W) Mutant in Complex With the Partial Agonist Kainic Acid at 2.1 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A Binding Site Tyrosine Shapes Desensitization Kinetics and Agonist Potency at GluR2: a mutagenic, kinetic, and crystallographic study

Holm, M.M.Naur, P.Vestergaard, B.Geballe, M.T.Gajhede, M.Kastrup, J.S.Traynelis, S.F.Egebjerg, J.

(2005) J Biol Chem 280: 35469-35476

  • DOI: 10.1074/jbc.M507800200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Binding of an agonist to the 2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)-propionic acid (AMPA) receptor family of the glutamate receptors (GluRs) results in rapid activation of an ion channel. Continuous application results in a non-desensitizing res ...

    Binding of an agonist to the 2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)-propionic acid (AMPA) receptor family of the glutamate receptors (GluRs) results in rapid activation of an ion channel. Continuous application results in a non-desensitizing response for agonists like kainate, whereas most other agonists, such as the endogenous agonist (S)-glutamate, induce desensitization. We demonstrate that a highly conserved tyrosine, forming a wedge between the agonist and the N-terminal part of the bi-lobed ligand-binding site, plays a key role in the receptor kinetics as well as agonist potency and selectivity. The AMPA receptor GluR2, with mutations in Tyr-450, were expressed in Xenopus laevis oocytes and characterized in a two-electrode voltage clamp setup. The mutation GluR2(Y450A) renders the receptor highly kainate selective, and rapid application of kainate to outside-out patches induced strongly desensitizing currents. When Tyr-450 was substituted with the larger tryptophan, the (S)-glutamate desensitization is attenuated with a 10-fold increase in steady-state/peak currents (19% compared with 1.9% at the wild type). Furthermore, the tryptophan mutant was introduced into the GluR2-S1S2J ligand binding core construct and co-crystallized with kainate, and the 2.1-A x-ray structure revealed a slightly more closed ligand binding core as compared with the wild-type complex. Through genetic manipulations combined with structural and electrophysiological analysis, we report that mutations in position 450 invert the potency of two central agonists while concurrently strongly shaping the agonist efficacy and the desensitization kinetics of the AMPA receptor GluR2.


    Related Citations: 
    • Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: crystal structures of the GluR2 ligand binding core.
      Armstrong, N., Gouaux, E.
      (2000) Neuron 28: 165
    • Tyr702 is an important determinant of agonist binding and domain closure of the ligand-binding core of GluR2.
      Frandsen, A., Pickering, D.S., Vestergaard, B., Kasper, C., Nielsen, B.B., Greenwood, J.R., Campiani, G., Fattorusso, C., Gajhede, M., Schousboe, A., Kastrup, J.S.
      (2005) Mol Pharmacol 67: 703
    • Tuning Activation of the Ampa-Sensitive Glur2 Ion Channel by Genetic Adjustment of Agonist-Induced
      Armstrong, N., Mayer, M., Gouaux, E.
      (2003) Proc Natl Acad Sci U S A 100: 5736

    Organizational Affiliation

    Department of Molecular Biology, C. F. Møllers Allé Bldg. 130, University of Aarhus, DK-8000 Aarhus, Denmark. mmh@fi.au.dk



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
A
263Rattus norvegicusMutation(s): 1 
Gene Names: Gria2Glur2
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KAI
Query on KAI

Download CCD File 
A
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE
C10 H15 N O4
VLSMHEGGTFMBBZ-OOZYFLPDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KAIKi:  3690   nM  BindingDB
KAIEC50:  26610   nM  BindingDB
KAIKi:  2630   nM  BindingDB
KAIKi:  8050   nM  BindingDB
KAIEC50:  380000   nM  BindingDB
KAIKi:  477   nM  BindingDB
KAIKi:  1980   nM  BindingDB
KAIKi:  12200   nM  BindingDB
KAIKi:  12221   nM  BindingDB
KAIEC50:  23000   nM  BindingDB
KAIKi:  5780   nM  BindingDB
KAIEC50:  27000   nM  BindingDB
KAIEC50:  47000   nM  BindingDB
KAIKi:  1.7999999523162842   nM  BindingDB
KAIEC50:  40000   nM  BindingDB
KAIEC50:  10570   nM  BindingDB
KAIKi:  3570   nM  BindingDB
KAIKi:  6300   nM  BindingDB
KAIEC50:  31000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.254α = 90
b = 61.635β = 90
c = 48.751γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-30
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-02
    Changes: Data collection, Refinement description, Source and taxonomy
  • Version 1.4: 2017-10-11
    Changes: Refinement description