1LBB

Crystal structure of the GluR2 ligand binding domain mutant (S1S2J-N754D) in complex with kainate at 2.1 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of glutamate receptor desensitization.

Sun, Y.Olson, R.Horning, M.Armstrong, N.Mayer, M.Gouaux, E.

(2002) Nature 417: 245-253

  • DOI: 10.1038/417245a
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ligand-gated ion channels transduce chemical signals into electrical impulses by opening a transmembrane pore in response to binding one or more neurotransmitter molecules. After activation, many ligand-gated ion channels enter a desensitized state i ...

    Ligand-gated ion channels transduce chemical signals into electrical impulses by opening a transmembrane pore in response to binding one or more neurotransmitter molecules. After activation, many ligand-gated ion channels enter a desensitized state in which the neurotransmitter remains bound but the ion channel is closed. Although receptor desensitization is crucial to the functioning of many ligand-gated ion channels in vivo, the molecular basis of this important process has until now defied analysis. Using the GluR2 AMPA-sensitive glutamate receptor, we show here that the ligand-binding cores form dimers and that stabilization of the intradimer interface by either mutations or allosteric modulators reduces desensitization. Perturbations that destabilize the interface enhance desensitization. Receptor activation involves conformational changes within each subunit that result in an increase in the separation of portions of the receptor that are linked to the ion channel. Our analysis defines the dimer interface in the resting and activated state, indicates how ligand binding is coupled to gating, and suggests modes of dimer dimer interaction in the assembled tetramer. Desensitization occurs through rearrangement of the dimer interface, which disengages the agonist-induced conformational change in the ligand-binding core from the ion channel gate.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, New York 10032, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamine receptor 2
A
263Rattus norvegicusMutation(s): 1 
Gene Names: GluR-2
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
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:  5780   nM  BindingDB
KAIKi:  6300   nM  BindingDB
KAIKi:  8050   nM  BindingDB
KAIKi:  1980   nM  BindingDB
KAIEC50:  60000   nM  BindingDB
KAIKi:  1.7999999523162842   nM  BindingDB
KAIEC50:  73000   nM  BindingDB
KAIKi:  7449   nM  BindingDB
KAIKi:  7450   nM  BindingDB
KAIKi:  7500   nM  BindingDB
KAIKi:  2630   nM  BindingDB
KAIEC50:  10570   nM  BindingDB
KAIEC50:  31000   nM  BindingDB
KAIKi:  3570   nM  BindingDB
KAIEC50:  26610   nM  BindingDB
KAIEC50:  380000   nM  BindingDB
KAIKi:  3690   nM  BindingDB
KAIEC50:  7510   nM  BindingDB
KAIEC50:  47000   nM  BindingDB
KAIKi:  12200   nM  BindingDB
KAIKi:  12221   nM  BindingDB
KAIEC50:  40000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.99α = 90
b = 63.27β = 92.25
c = 46.51γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-05
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-16
    Changes: Refinement description, Source and taxonomy