3EPE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

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, B
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
GLU
Query on GLU

Download CCD File 
A, B
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GGLEC50:  14000   nM  BindingDB
GGLEC50:  14700   nM  BindingDB
GGLKi:  336   nM  BindingDB
GGLKi:  10000   nM  BindingDB
GGLEC50:  2260   nM  BindingDB
GGLEC50:  190000   nM  BindingDB
GGLKi:  1360   nM  BindingDB
GGLKi:  500   nM  BindingDB
GGLEC50:  21200   nM  BindingDB
GGLEC50:  1300   nM  BindingDB
GGLKi:  7400   nM  BindingDB
GGLEC50:  140000   nM  BindingDB
GGLKi:  280   nM  BindingDB
GGLKi:  282   nM  BindingDB
GGLKi:  354   nM  BindingDB
GGLEC50:  71000   nM  BindingDB
GGLKi:  62   nM  BindingDB
GGLEC50:  28000   nM  BindingDB
GGLKi:  868   nM  BindingDB
GGLEC50:  35000   nM  BindingDB
GGLEC50:  3660   nM  BindingDB
GGLKi:  89   nM  BindingDB
GGLEC50:  52000   nM  BindingDB
GGLKi:  940   nM  BindingDB
GGLEC50:  2190   nM  BindingDB
GGLEC50:  17000   nM  BindingDB
GGLEC50:  67000   nM  BindingDB
GGLEC50:  19600   nM  BindingDB
GGLEC50:  20000   nM  BindingDB
GGLEC50:  22000   nM  BindingDB
GGLEC50:  6200   nM  BindingDB
GGLEC50:  100000   nM  BindingDB
GGLKi:  249   nM  BindingDB
GGLKi:  254   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.374α = 90
b = 105.124β = 97.26
c = 66.336γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-09-29 
  • 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: Version format compliance
  • Version 1.2: 2017-07-26
    Changes: Advisory, Refinement description, Source and taxonomy
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description