2F35

Crystal Structure of the GluR5 Ligand Binding Core with UBP302 At 1.87 Angstroms Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 2852-2861

  • DOI: 10.1523/JNEUROSCI.0123-06.2005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glutamate receptor (GluR) ion channels mediate fast synaptic transmission in the mammalian CNS. Numerous crystallographic studies, the majority on the GluR2-subtype AMPA receptor, have revealed the structural basis for binding of subtype-specific ago ...

    Glutamate receptor (GluR) ion channels mediate fast synaptic transmission in the mammalian CNS. Numerous crystallographic studies, the majority on the GluR2-subtype AMPA receptor, have revealed the structural basis for binding of subtype-specific agonists. In contrast, because there are far fewer antagonist-bound structures, the mechanisms for antagonist binding are much less well understood, particularly for kainate receptors that exist as multiple subtypes with a distinct biology encoded by the GluR5-7, KA1, and KA2 genes. We describe here high-resolution crystal structures for the GluR5 ligand-binding core complex with UBP302 and UBP310, novel GluR5-selective antagonists. The crystal structures reveal the structural basis for the high selectivity for GluR5 observed in radiolabel displacement assays for the isolated ligand binding cores of the GluR2, GluR5, and GluR6 subunits and during inhibition of glutamate-activated currents in studies on full-length ion channels. The antagonists bind via a novel mechanism and do not form direct contacts with the E723 side chain as occurs in all previously solved AMPA and kainate receptor agonist and antagonist complexes. This results from a hyperextension of the ligand binding core compared with previously solved structures. As a result, in dimer assemblies, there is a 22 A extension of the ion channel linkers in the transition from antagonist- to glutamate-bound forms. This large conformational change is substantially different from that described for AMPA receptors, was not possible to predict from previous work, and suggests that glutamate receptors are capable of much larger movements than previously thought.


    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


    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. mayerm@mail.nih.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
A, B
258Rattus norvegicusMutation(s): 1 
Gene Names: Grik1 (Glur5)
Find proteins for P22756 (Rattus norvegicus)
Go to UniProtKB:  P22756
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
UBC
Query on UBC

Download SDF File 
Download CCD File 
A, B
(S)-1-(2-AMINO-2-CARBOXYETHYL)-3-(2-CARBOXYBENZYL)PYRIMIDINE-2,4-DIONE
C15 H15 N3 O6
UUIYULWYHDSXHL-NSHDSACASA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A, B
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UBCKd: 3940 nM BINDINGMOAD
UBCKd: 3940 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 97.876α = 90.00
b = 97.907β = 90.00
c = 128.347γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-11-18 
  • Released Date: 2006-04-04 
  • Deposition Author(s): Mayer, M.L.

Revision History 

  • Version 1.0: 2006-04-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-08-16
    Type: Source and taxonomy