1FTK

CRYSTAL STRUCTURE OF THE GLUR2 LIGAND BINDING CORE (S1S2I) IN COMPLEX WITH KAINATE AT 1.6 A RESOLUTION

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    1FTJ, 1FTK, 1FTL, 1FTM, 1FTO, 1FW0

  • 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 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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUTAMATE RECEPTOR SUBUNIT 2A279Rattus norvegicusMutation(s): 0 
Gene Names: Gria2
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19491
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 Ideal Coordinates CCD File 
B [auth A]3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE
C10 H15 N O4
VLSMHEGGTFMBBZ-OOZYFLPDSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
KAI BindingDB:  1FTK Ki: min: 1.8, max: 1.22e+4 (nM) from 11 assay(s)
EC50: min: 1.06e+4, max: 3.80e+5 (nM) from 8 assay(s)
Binding MOAD:  1FTK IC50: 1.45e+4 (nM) from 1 assay(s)
PDBBind:  1FTK IC50: 1.45e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.36α = 90
b = 63.12β = 92.79
c = 46.38γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: Advisory, Refinement description, Source and taxonomy