1FTJ

CRYSTAL STRUCTURE OF THE GLUR2 LIGAND BINDING CORE (S1S2J) IN COMPLEX WITH GLUTAMATE AT 1.9 RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.275 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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: 165-181

  • DOI: 10.1016/s0896-6273(00)00094-5
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Crystal structures of the GluR2 ligand binding core (S1S2) have been determined in the apo state and in the presence of the antagonist DNQX, the partial agonist kainate, and the full agonists AMPA and glutamate. The domains of the S1S2 ligand binding ...

    Crystal structures of the GluR2 ligand binding core (S1S2) have been determined in the apo state and in the presence of the antagonist DNQX, the partial agonist kainate, and the full agonists AMPA and glutamate. The domains of the S1S2 ligand binding core are expanded in the apo state and contract upon ligand binding with the extent of domain separation decreasing in the order of apo > DNQX > kainate > glutamate approximately equal to AMPA. These results suggest that agonist-induced domain closure gates the transmembrane channel and the extent of receptor activation depends upon the degree of domain closure. AMPA and glutamate also promote a 180 degrees flip of a trans peptide bond in the ligand binding site. The crystal packing of the ligand binding cores suggests modes for subunit-subunit contact in the intact receptor and mechanisms by which allosteric effectors modulate receptor activity.


    Related Citations: 
    • Probing the ligand binding domain of the GluR2 receptor by proteolysis and deletion mutagenesis defines domain boundaries and yields a crystallizable construct.
      Chen, G.Q., Sun, Y., Jin, R., Gouaux, E.
      (1998) Protein Sci 7: 2623

    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMATE RECEPTOR SUBUNIT 2
A, B, C
263Rattus norvegicusMutation(s): 0 
Gene Names: Gria2
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

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

Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GGLKi:  62   nM  BindingDB
GGLKi:  940   nM  BindingDB
GGLEC50:  2190   nM  BindingDB
GGLEC50:  35000   nM  BindingDB
GGLKi:  280   nM  BindingDB
GGLKi:  282   nM  BindingDB
GGLEC50:  190000   nM  BindingDB
GGLEC50:  140000   nM  BindingDB
GGLEC50:  67000   nM  BindingDB
GGLEC50:  14000   nM  BindingDB
GGLEC50:  14700   nM  BindingDB
GGLEC50:  3660   nM  BindingDB
GGLKi:  89   nM  BindingDB
GGLEC50:  52000   nM  BindingDB
GGLKi:  249   nM  BindingDB
GGLKi:  254   nM  BindingDB
GGLEC50:  140000   nM  BindingDB
GLUIC50:  821   nM  Binding MOAD
GGLEC50:  22000   nM  BindingDB
GGLKi:  10000   nM  BindingDB
GGLEC50:  6200   nM  BindingDB
GGLEC50:  100000   nM  BindingDB
GLUIC50 :  821   nM  PDBBind
GGLKi:  500   nM  BindingDB
GGLEC50:  1300   nM  BindingDB
GGLEC50:  21200   nM  BindingDB
GGLKi:  7400   nM  BindingDB
GGLEC50:  71000   nM  BindingDB
GGLEC50:  17000   nM  BindingDB
GGLEC50:  19600   nM  BindingDB
GGLEC50:  20000   nM  BindingDB
GGLKi:  336   nM  BindingDB
GGLKi:  354   nM  BindingDB
GGLEC50:  2260   nM  BindingDB
GGLKi:  1360   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.275 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.002α = 90
b = 163.363β = 90
c = 47.396γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation