PDBsum entry 3g3f

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protein ligands metals Protein-protein interface(s) links
Membrane protein PDB id
Protein chains
251 a.a. *
GLU ×2
IPA ×2
_NA ×4
Waters ×581
* Residue conservation analysis
PDB id:
Name: Membrane protein
Title: Crystal structure of the glur6 ligand binding domain dimer with glutamate and nacl at 1.38 angstrom resolution
Structure: Glutamate receptor, ionotropic kainate 2. Chain: a, b. Fragment: residues 429-544, 667-806. Synonym: glutamate receptor 6, glur-6, glur6. Engineered: yes
Source: Rattus norvegicus. Brown rat,rat,rats. Organism_taxid: 10116. Gene: glur6, grik2. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.38Å     R-factor:   0.153     R-free:   0.175
Authors: C.Chaudhry,M.L.Mayer
Key ref: C.Chaudhry et al. (2009). Stability of ligand-binding domain dimer assembly controls kainate receptor desensitization. EMBO J, 28, 1518-1530. PubMed id: 19339989
02-Feb-09     Release date:   02-Jun-09    
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Protein chains
Pfam   ArchSchema ?
P42260  (GRIK2_RAT) -  Glutamate receptor ionotropic, kainate 2
908 a.a.
251 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biochemical function     ionotropic glutamate receptor activity     2 terms  


EMBO J 28:1518-1530 (2009)
PubMed id: 19339989  
Stability of ligand-binding domain dimer assembly controls kainate receptor desensitization.
C.Chaudhry, M.C.Weston, P.Schuck, C.Rosenmund, M.L.Mayer.
AMPA and kainate receptors mediate fast synaptic transmission. AMPA receptor ligand-binding domains form dimers, which are key functional units controlling ion-channel activation and desensitization. Dimer stability is inversely related to the rate and extent of desensitization. Kainate and AMPA receptors share common structural elements, but functional measurements suggest that subunit assembly and gating differs between these subtypes. To investigate this, we constructed a library of GluR6 kainate receptor mutants and directly measured changes in kainate receptor dimer stability by analytical ultracentrifugation, which, combined with electrophysiological experiments, revealed an inverse correlation between dimer stability and the rate of desensitization. We solved crystal structures for a series of five GluR6 mutants, to understand the molecular mechanisms for dimer stabilization. We demonstrate that the desensitized state of kainate receptors acts as a deep energy well offsetting the stabilizing effects of dimer interface mutants, and that the deactivation of kainate receptor responses is dominated by entry into desensitized states. Our results show how neurotransmitter receptors with similar structures and gating mechanisms can exhibit strikingly different functional properties.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21372852 M.L.Mayer (2011).
Glutamate receptor ion channels: where do all the calories go?
  Nat Struct Mol Biol, 18, 253-254.  
21349697 M.L.Mayer (2011).
Structure and mechanism of glutamate receptor ion channel assembly, activation and modulation.
  Curr Opin Neurobiol, 21, 283-290.  
21167941 R.Ghirlando (2011).
The analysis of macromolecular interactions by sedimentation equilibrium.
  Methods, 54, 145-156.  
20881961 T.Nogi, N.Yasui, E.Mihara, Y.Matsunaga, M.Noda, N.Yamashita, T.Toyofuku, S.Uchiyama, Y.Goshima, A.Kumanogoh, and J.Takagi (2010).
Structural basis for semaphorin signalling through the plexin receptor.
  Nature, 467, 1123-1127.
PDB codes: 3afc 3al8 3al9
20404149 U.Das, J.Kumar, M.L.Mayer, and A.J.Plested (2010).
Domain organization and function in GluK2 subtype kainate receptors.
  Proc Natl Acad Sci U S A, 107, 8463-8468.  
19617541 C.Chaudhry, A.J.Plested, P.Schuck, and M.L.Mayer (2009).
Energetics of glutamate receptor ligand binding domain dimer assembly are modulated by allosteric ions.
  Proc Natl Acad Sci U S A, 106, 12329-12334.  
19561126 N.Nayeem, Y.Zhang, D.K.Schweppe, D.R.Madden, and T.Green (2009).
A nondesensitizing kainate receptor point mutant.
  Mol Pharmacol, 76, 534-542.  
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