2PBW

Crystal Structure of the Ligand-Binding Core of iGluR5 in Complex with the Partial agonist Domoic Acid at 2.5 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Partial agonism and antagonism of the ionotropic glutamate receptor iGLuR5: structures of the ligand-binding core in complex with domoic acid and 2-amino-3-[5-tert-butyl-3-(phosphonomethoxy)-4-isoxazolyl]propionic acid.

Hald, H.Naur, P.Pickering, D.S.Sprogoe, D.Madsen, U.Timmermann, D.B.Ahring, P.K.Liljefors, T.Schousboe, A.Egebjerg, J.Gajhede, M.Kastrup, J.S.

(2007) J.Biol.Chem. 282: 25726-25736

  • DOI: 10.1074/jbc.M700137200
  • Primary Citation of Related Structures:  1VSO

  • PubMed Abstract: 
  • More than 50 structures have been reported on the ligand-binding core of the ionotropic glutamate receptor iGluR2 that belongs to the 2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid-type of receptors. In contrast, the ligand-binding core of ...

    More than 50 structures have been reported on the ligand-binding core of the ionotropic glutamate receptor iGluR2 that belongs to the 2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid-type of receptors. In contrast, the ligand-binding core of the kainic acid-type receptor iGluR5 has only been crystallized with three different ligands. Hence, additional structures of iGluR5 are needed to broaden the understanding of the ligand-binding properties of iGluR5, and the conformational changes leading to channel opening and closing. Here, we present two structures of the ligand-binding core of iGluR5; one as a complex with the partial agonist (2S,3S,4S)-3-carboxymethyl-4-[(1Z,3E,5R)-5-carboxy-1-methyl-hexa-1,3-dienyl]-pyrrolidine-2-carboxylic acid (domoic acid) and one as a complex with the antagonist (S)-2-amino-3-[5-tert-butyl-3-(phosphonomethoxy)-4-isoxazolyl]propionic acid ((S)-ATPO). In agreement with the partial agonist activity of domoic acid, the ligand-binding core of the iGluR5 complex is stabilized by domoic acid in a conformation that is 11 degrees more open than the conformation observed in the full agonist (S)-glutamic acid complex. This is primarily caused by the 5-carboxy-1-methyl-hexa-1,3-dienyl moiety of domoic acid and residues Val685-Thr690 of iGluR5. An even larger domain opening of 28 degrees is introduced upon binding of the antagonist (S)-ATPO. It appears that the span of domain opening is much larger in the ligand-binding core of iGluR5 (30 degrees) compared with what has been observed in iGluR2 (19 degrees ). Similarly, much larger variation in the distances between transmembrane linker residues in the two protomers comprising the dimer is observed in iGluR5 as compared with iGluR2.


    Related Citations: 
    • Crystal structures of the kainate receptor GluR5 ligand binding core dimer with novel GluR5-selective antagonists.
      Mayer, M.L.,Ghosal, A.,Dolman, N.P.,Jane, D.E.
      (2006) J.Neurosci. 26: 2852
    • Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate.
      Naur, P.,Vestergaard, B.,Skov, L.K.,Egebjerg, J.,Gajhede, M.,Kastrup, J.S.
      (2005) FEBS Lett. 579: 1154
    • Structure of the kainate receptor subunit GluR6 agonist-binding domain complexed with domoic acid.
      Nanao, M.H.,Green, T.,Stern-Bach, Y.,Heinemann, S.F.,Choe, S.
      (2005) Proc.Natl.Acad.Sci.USA 102: 1708


    Organizational Affiliation

    Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor, ionotropic kainate 1
A, B
257Rattus norvegicusGene Names: Grik1 (Glur5)
Find proteins for P22756 (Rattus norvegicus)
Go to UniProtKB:  P22756
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DOQ
Query on DOQ

Download SDF File 
Download CCD File 
A, B
(2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID
(2S,3S,4S)-3-CARBOXYMETHYL-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-HEXA-1,3-DIENYL]-PYRROLIDINE-2-CARBOXYLIC ACID; DOMOIC ACID
C15 H21 N O6
VZFRNCSOCOPNDB-AOKDLOFSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DOQKi: 5.56 nM BINDINGMOAD
DOQKi: 5.56 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.863α = 90.00
b = 70.863β = 90.00
c = 233.168γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2007-10-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-06-13
    Type: Other
  • Version 1.4: 2017-08-02
    Type: Refinement description, Source and taxonomy
  • Version 1.5: 2017-10-18
    Type: Refinement description