X-ray structure of the GluR6 ligand binding core (S1S2A) in complex with glutamate at 1.65 A resolution

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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Crystal structures of the GluR5 and GluR6 ligand binding cores: Molecular mechanisms underlying kainate receptor selectivity

Mayer, M.L.

(2005) Neuron 45: 539-552

  • DOI: https://doi.org/10.1016/j.neuron.2005.01.031
  • Primary Citation of Related Structures:  
    1S50, 1S7Y, 1S9T, 1SD3, 1TT1, 1TXF

  • PubMed Abstract: 

    Little is known about the molecular mechanisms underlying differences in the ligand binding properties of AMPA, kainate, and NMDA subtype glutamate receptors. Crystal structures of the GluR5 and GluR6 kainate receptor ligand binding cores in complexes with glutamate, 2S,4R-4-methylglutamate, kainate, and quisqualate have now been solved. The structures reveal that the ligand binding cavities are 40% (GluR5) and 16% (GluR6) larger than for GluR2. The binding of AMPA- and GluR5-selective agonists to GluR6 is prevented by steric occlusion, which also interferes with the high-affinity binding of 2S,4R-4-methylglutamate to AMPA receptors. Strikingly, the extent of domain closure produced by the GluR6 partial agonist kainate is only 3 degrees less than for glutamate and 11 degrees greater than for the GluR2 kainate complex. This, together with extensive interdomain contacts between domains 1 and 2 of GluR5 and GluR6, absent from AMPA receptors, likely contributes to the high stability of GluR5 and GluR6 kainate complexes.

  • Organizational Affiliation

    Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA. mlm@helix.nih.gov

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate Receptor 6259Rattus norvegicusMutation(s): 2 
Gene Names: GluR6 residues 398-513 and 636-775
Find proteins for P42260 (Rattus norvegicus)
Explore P42260 
Go to UniProtKB:  P42260
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42260
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GLU

Download Ideal Coordinates CCD File 
C5 H9 N O4
Binding Affinity Annotations 
IDSourceBinding Affinity
GLU PDBBind:  1S50 Ki: 63 (nM) from 1 assay(s)
Binding MOAD:  1S50 Ki: 1400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.272α = 90
b = 52.272β = 90
c = 169.411γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2005-02-08 
  • Deposition Author(s): Mayer, M.L.

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-26
    Changes: Advisory, Refinement description, Source and taxonomy
  • Version 1.4: 2021-10-27
    Changes: Advisory, Database references, Derived calculations
  • Version 1.5: 2023-08-23
    Changes: Data collection, Refinement description