1P1N

GluR2 Ligand Binding Core (S1S2J) Mutant L650T in Complex with Kainate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Tuning activation of the AMPA-sensitive GluR2 ion channel by genetic adjustment of agonist-induced conformational changes.

Armstrong, N.Mayer, M.Gouaux, E.

(2003) Proc Natl Acad Sci U S A 100: 5736-5741

  • DOI: 10.1073/pnas.1037393100
  • Primary Citation of Related Structures:  
    1P1Q, 1P1O, 1P1N, 1P1W, 1P1U

  • PubMed Abstract: 
  • The (S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazole) propionic acid (AMPA) receptor discriminates between agonists in terms of binding and channel gating; AMPA is a high-affinity full agonist, whereas kainate is a low-affinity partial agonist. Although ...

    The (S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazole) propionic acid (AMPA) receptor discriminates between agonists in terms of binding and channel gating; AMPA is a high-affinity full agonist, whereas kainate is a low-affinity partial agonist. Although there is extensive literature on the functional characterization of partial agonist activity in ion channels, structure-based mechanisms are scarce. Here we investigate the role of Leu-650, a binding cleft residue conserved among AMPA receptors, in maintaining agonist specificity and regulating agonist binding and channel gating by using physiological, x-ray crystallographic, and biochemical techniques. Changing Leu-650 to Thr yields a receptor that responds more potently and efficaciously to kainate and less potently and efficaciously to AMPA relative to the WT receptor. Crystal structures of the Leu-650 to Thr mutant reveal an increase in domain closure in the kainate-bound state and a partially closed and a fully closed conformation in the AMPA-bound form. Our results indicate that agonists can induce a range of conformations in the GluR2 ligand-binding core and that domain closure is directly correlated to channel activation. The partially closed, AMPA-bound conformation of the L650T mutant likely captures the structure of an agonist-bound, inactive state of the receptor. Together with previously solved structures, we have determined a mechanism of agonist binding and subsequent conformational rearrangements.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics and Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2A263Rattus norvegicusMutation(s): 1 
Gene Names: GRIA2 OR GLUR2
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Protein Feature View
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  • 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 %)
KAIEC50:  31000   nM  BindingDB
KAIEC50:  380000   nM  BindingDB
KAIKi:  2630   nM  BindingDB
KAIEC50:  10570   nM  BindingDB
KAIEC50:  40000   nM  BindingDB
KAIKi:  7449   nM  BindingDB
KAIKi:  7450   nM  BindingDB
KAIKi:  7500   nM  BindingDB
KAIEC50:  7510   nM  BindingDB
KAIKd:  160   nM  Binding MOAD
KAIKi:  3690   nM  BindingDB
KAIKi:  8050   nM  BindingDB
KAIKi:  12200   nM  BindingDB
KAIKi:  12221   nM  BindingDB
KAIKi:  1980   nM  BindingDB
KAIEC50:  47000   nM  BindingDB
KAIKi:  5780   nM  BindingDB
KAIKi:  6300   nM  BindingDB
KAIEC50:  60000   nM  BindingDB
KAIKi:  1.7999999523162842   nM  BindingDB
KAIKi:  3570   nM  BindingDB
KAIEC50:  26610   nM  BindingDB
KAIEC50:  73000   nM  BindingDB
KAIKd :  160   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.268 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.386α = 90
b = 88.741β = 90
c = 48.151γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-10
    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: 2017-08-16
    Changes: Refinement description, Source and taxonomy