3T96

Iodowillardiine bound to a double cysteine mutant (A452C/S652C) of the ligand binding domain of GluA2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of AMPA Receptor Activation by Partial Agonists: DISULFIDE TRAPPING OF CLOSED LOBE CONFORMATIONS.

Ahmed, A.H.Wang, S.Chuang, H.H.Oswald, R.E.

(2011) J Biol Chem 286: 35257-35266

  • DOI: 10.1074/jbc.M111.269001
  • Primary Citation of Related Structures:  
    3T93, 3T96, 3T9U, 3T9V, 3T9H, 3T9X

  • PubMed Abstract: 
  • The mechanism by which agonist binding to an ionotropic glutamate receptor leads to channel opening is a central issue in molecular neurobiology. Partial agonists are useful tools for studying the activation mechanism because they produce full channel activation with lower probability than full agonists ...

    The mechanism by which agonist binding to an ionotropic glutamate receptor leads to channel opening is a central issue in molecular neurobiology. Partial agonists are useful tools for studying the activation mechanism because they produce full channel activation with lower probability than full agonists. Structural transitions that determine the efficacy of partial agonists can provide information on the trigger that begins the channel-opening process. The ligand-binding domain of AMPA receptors is a bilobed structure, and the closure of the lobes is associated with channel activation. One possibility is that partial agonists sterically block full lobe closure but that partial degrees of closure trigger the channel with a lower probability. Alternatively, full lobe closure may be required for activation, and the stability of the fully closed state could determine efficacy with the fully closed state having a lower stability when bound to partial relative to full agonists. Disulfide-trapping experiments demonstrated that even extremely low efficacy ligands such as 6-cyano-7-nitroquinoxaline-2,3-dione can produce a full lobe closure, presumably with low probability. The results are consistent the hypothesis that the efficacy is determined at least in part by the stability of the state in which the lobes are fully closed.


    Organizational Affiliation

    Department of Molecular Medicine, Cornell University, Ithaca, New York 14853, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2A [auth B], B [auth D], C [auth F]258Rattus norvegicusMutation(s): 2 
Gene Names: Gria2GluA2
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Protein Feature View
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  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IWDKi:  105   nM  BindingDB
IWDKi:  163   nM  BindingDB
IWDKi:  738   nM  BindingDB
IWDKi:  976   nM  BindingDB
IWDKi:  176   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.793α = 90
b = 114.351β = 90
c = 163.547γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHENIXmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2011-08-31
    Changes: Database references
  • Version 1.2: 2011-10-19
    Changes: Database references
  • Version 1.3: 2017-07-26
    Changes: Source and taxonomy