3C32

Crystal structure of GluR5 ligand-binding core in complex with sodium at 1.72 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular basis of kainate receptor modulation by sodium.

Plested, A.J.Vijayan, R.Biggin, P.C.Mayer, M.L.

(2008) Neuron 58: 720-735

  • DOI: 10.1016/j.neuron.2008.04.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Membrane proteins function in a polarized ionic environment with sodium-rich extracellular and potassium-rich intracellular solutions. Glutamate receptors that mediate excitatory synaptic transmission in the brain show unusual sensitivity to external ...

    Membrane proteins function in a polarized ionic environment with sodium-rich extracellular and potassium-rich intracellular solutions. Glutamate receptors that mediate excitatory synaptic transmission in the brain show unusual sensitivity to external ions, resulting in an apparent requirement for sodium in order for glutamate to activate kainate receptors. Here, we solve the structure of the Na(+)-binding sites and determine the mechanism by which allosteric anions and cations regulate ligand-binding dimer stability, and hence the rate of desensitization and receptor availability for gating by glutamate. We establish a stoichiometry for binding of 2 Na(+) to 1 Cl(-) and show that allosteric anions and cations bind at physically discrete sites with strong electric fields, that the binding sites are not saturated in CSF, and that the requirement of kainate receptors for Na(+) occurs simply because other cations bind with lower affinity and have lower efficacy compared to Na(+).


    Related Citations: 
    • Crystal structures of the GluR5 and GluR6 ligand binding cores: molecular mechanisms underlying kainate receptor selectivity.
      Mayer, M.L.
      (2005) Neuron 45: 539
    • Structure and mechanism of kainate receptor modulation by anions.
      Plested, A.J.,Mayer, M.L.
      (2007) Neuron 53: 829


    Organizational Affiliation

    Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, NICHD, NIH, DHHS, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
A, B
258Rattus norvegicusMutation(s): 0 
Gene Names: Grik1 (Glur5)
Find proteins for P22756 (Rattus norvegicus)
Go to UniProtKB:  P22756
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
KAI
Query on KAI

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A, B
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE
KAINATE
C10 H15 N O4
VLSMHEGGTFMBBZ-OOZYFLPDSA-N
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KAIEC50: 16200 nM (96) BINDINGDB
KAIKi: 177 nM (96) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.546α = 90.00
b = 70.546β = 90.00
c = 234.456γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-01-27 
  • Released Date: 2008-06-17 
  • Deposition Author(s): Mayer, M.L.

Revision History 

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-08-02
    Type: Source and taxonomy
  • Version 1.3: 2017-10-25
    Type: Refinement description