3EN3

Crystal Structure of the GluR4 Ligand-Binding domain in complex with kainate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Correlating AMPA receptor activation and cleft closure across subunits: crystal structures of the GluR4 ligand-binding domain in complex with full and partial agonists

Gill, A.Birdsey-Benson, A.Jones, B.L.Henderson, L.P.Madden, D.R.

(2008) Biochemistry 47: 13831-13841

  • DOI: 10.1021/bi8013196
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • AMPA receptors are glutamate-gated ion channels that are essential mediators of synaptic signals in the central nervous system. They form tetramers that are assembled as combinations of subunits GluR1-4, each of which contains a ligand-binding domain ...

    AMPA receptors are glutamate-gated ion channels that are essential mediators of synaptic signals in the central nervous system. They form tetramers that are assembled as combinations of subunits GluR1-4, each of which contains a ligand-binding domain (LBD). Crystal structures of the GluR2 LBD have revealed an agonist-binding cleft, which is located between two lobes and which acts like a Venus flytrap. In general, agonist efficacy is correlated with the extent of cleft closure. However, recent observations show that cleft closure is not the sole determinant of the relative efficacy for glutamate receptors. In addition, these studies have focused on the GluR2 subunit, which is the specific target of a physiologically important RNA-editing modification in vivo. We therefore sought to test the generality of the cleft closure-efficacy correlation for other AMPA-R subunits. Here, we present crystal structures of the GluR4(flip) LBD in complex with both full and partial agonists. As for GluR2, both agonists stabilize a closed-cleft conformation, and the partial agonist induces a smaller cleft closure than the full agonist. However, a detailed analysis of LBD-kainate interactions reveals the importance of subtle backbone conformational changes in the ligand-binding pocket in determining the magnitude of agonist-associated conformational changes. Furthermore, the GluR4 subunit exhibits a different correlation between receptor activation and LBD cleft closure than does GluR2.


    Organizational Affiliation

    Departments of Biochemistry and Physiology, Dartmouth Medical School, 7200 Vail Building, Hanover, New Hampshire 03755, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 4,Glutamate receptor
A
257Rattus norvegicusMutation(s): 6 
Gene Names: Glur4Glutamate receptor
Find proteins for P19493 (Rattus norvegicus)
Go to UniProtKB:  P19493
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KAI
Query on KAI

Download CCD File 
A
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE
C10 H15 N O4
VLSMHEGGTFMBBZ-OOZYFLPDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KAIKi:  1.7999999523162842   nM  BindingDB
KAIEC50:  10570   nM  BindingDB
KAIKi:  3690   nM  BindingDB
KAIEC50:  7510   nM  BindingDB
KAIEC50:  40000   nM  BindingDB
KAIKi:  5780   nM  BindingDB
KAIEC50:  31000   nM  BindingDB
KAIKi:  3570   nM  BindingDB
KAIEC50:  26610   nM  BindingDB
KAIKi:  6300   nM  BindingDB
KAIKi:  1980   nM  BindingDB
KAIKi:  8050   nM  BindingDB
KAIEC50:  60000   nM  BindingDB
KAIEC50:  380000   nM  BindingDB
KAIKi:  2630   nM  BindingDB
KAIKi:  7449   nM  BindingDB
KAIKi:  7450   nM  BindingDB
KAIKi:  7500   nM  BindingDB
KAIEC50:  73000   nM  BindingDB
KAIEC50:  47000   nM  BindingDB
KAIKi:  12200   nM  BindingDB
KAIKi:  12221   nM  BindingDB
KAIKi:  1710   nM  BindingDB
KAIKi:  1714   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.906α = 90
b = 48.749β = 109.06
c = 47.766γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-09-25 
  • Released Date: 2009-05-19 
  • Deposition Author(s): Gill, A., Madden, D.R.

Revision History 

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2014-04-02
    Changes: Source and taxonomy
  • Version 1.3: 2017-07-26
    Changes: Advisory, Refinement description, Source and taxonomy