3B6W

Crystal Structure of the GLUR2 Ligand Binding Core (S1S2J) T686S Mutant in Complex with Glutamate at 1.7 Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and single-channel results indicate that the rates of ligand binding domain closing and opening directly impact AMPA receptor gating.

Zhang, W.Cho, Y.Lolis, E.Howe, J.R.

(2008) J Neurosci 28: 932-943

  • DOI: 10.1523/JNEUROSCI.3309-07.2008
  • Primary Citation of Related Structures:  
    3B6W, 3B6Q, 3B6T

  • PubMed Abstract: 
  • At most excitatory central synapses, glutamate is released from presynaptic terminals and binds to postsynaptic AMPA receptors, initiating a series of conformational changes that result in ion channel opening. Efficient transmission at these synapses ...

    At most excitatory central synapses, glutamate is released from presynaptic terminals and binds to postsynaptic AMPA receptors, initiating a series of conformational changes that result in ion channel opening. Efficient transmission at these synapses requires that glutamate binding to AMPA receptors results in rapid and near-synchronous opening of postsynaptic receptor channels. In addition, if the information encoded in the frequency of action potential discharge is to be transmitted faithfully, glutamate must dissociate from the receptor quickly, enabling the synapse to discriminate presynaptic action potentials that are spaced closely in time. The current view is that the efficacy of agonists is directly related to the extent to which ligand binding results in closure of the binding domain. For glutamate to dissociate from the receptor, however, the binding domain must open. Previously, we showed that mutations in glutamate receptor subunit 2 that should destabilize the closed conformation not only sped deactivation but also altered the relative efficacy of glutamate and quisqualate. Here we present x-ray crystallographic and single-channel data that support the conclusions that binding domain closing necessarily precedes channel opening and that the kinetics of conformational changes at the level of the binding domain importantly influence ion channel gating. Our findings suggest that the stability of the closed-cleft conformation has been tuned during evolution so that glutamate dissociates from the receptor as rapidly as possible but remains an efficacious agonist.


    Related Citations: 
    • 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

    Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2ABCD263Rattus norvegicusMutation(s): 1 
Gene Names: Gria2Glur2
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

Download CCD File 
A, B
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GGLKi:  1360   nM  BindingDB
GGLKi:  7400   nM  BindingDB
GGLEC50:  19600   nM  BindingDB
GGLEC50:  1300   nM  BindingDB
GGLEC50:  20000   nM  BindingDB
GGLEC50:  17000   nM  BindingDB
GGLEC50:  2190   nM  BindingDB
GGLKi:  500   nM  BindingDB
GGLKi:  940   nM  BindingDB
GGLKi:  280   nM  BindingDB
GGLKi:  282   nM  BindingDB
GGLKi:  336   nM  BindingDB
GGLEC50:  2260   nM  BindingDB
GGLKi:  354   nM  BindingDB
GGLEC50:  140000   nM  BindingDB
GGLEC50:  14000   nM  BindingDB
GGLKi:  254   nM  BindingDB
GGLKi:  249   nM  BindingDB
GGLEC50:  190000   nM  BindingDB
GGLEC50:  22000   nM  BindingDB
GGLEC50:  100000   nM  BindingDB
GGLEC50:  14700   nM  BindingDB
GGLEC50:  140000   nM  BindingDB
GGLEC50:  67000   nM  BindingDB
GGLEC50:  3660   nM  BindingDB
GGLEC50:  52000   nM  BindingDB
GGLEC50:  6200   nM  BindingDB
GGLKi:  89   nM  BindingDB
GGLEC50:  35000   nM  BindingDB
GGLKi:  62   nM  BindingDB
GGLEC50:  21200   nM  BindingDB
GGLEC50:  71000   nM  BindingDB
GGLKi:  10000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.817α = 90
b = 95.84β = 93.43
c = 122.886γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CBASSdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-02
    Changes: Source and taxonomy