3C33

Crystal structure of GluR5 ligand-binding core in complex with potassium at 1.78 Angstrom resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.165 

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

    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
K
Query on K
Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
KAI
Query on KAI
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Download CCD File 
A, B
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE
KAINATE
C10 H15 N O4
VLSMHEGGTFMBBZ-OOZYFLPDSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL
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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KAIKi: 1.4 - 177 nM (96) BINDINGDB
KAIKd: 39 nM (88) BINDINGDB
KAIEC50: 1800 - 37000 nM (88) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.165 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.742α = 90.00
b = 70.742β = 90.00
c = 234.460γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots


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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