3KFM

Crystal Structure of the GluA4 Ligand-Binding domain L651V mutant in complex with kainate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Enhanced efficacy without further cleft closure: reevaluating twist as a source of agonist efficacy in AMPA receptors.

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

(2010) J Neurosci 30: 1463-1470

  • DOI: 10.1523/JNEUROSCI.4558-09.2010
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • AMPA receptors (AMPARs) are tetrameric ligand-gated ion channels that couple the energy of glutamate binding to the opening of a transmembrane channel. Crystallographic and electrophysiological analysis of AMPARs has suggested a coupling between (1) ...

    AMPA receptors (AMPARs) are tetrameric ligand-gated ion channels that couple the energy of glutamate binding to the opening of a transmembrane channel. Crystallographic and electrophysiological analysis of AMPARs has suggested a coupling between (1) cleft closure in the bilobate ligand-binding domain (LBD), (2) the resulting separation of transmembrane helix attachment points across subunit dimers, and (3) agonist efficacy. In general, more efficacious agonists induce greater degrees of cleft closure and transmembrane separation than partial agonists. Several apparent violations of the cleft-closure/efficacy paradigm have emerged, although in all cases, intradimer separation remains as the driving force for channel opening. Here, we examine the structural basis of partial agonism in GluA4 AMPARs. We find that the L651V substitution enhances the relative efficacy of kainate without increasing either LBD cleft closure or transmembrane separation. Instead, the conformational change relative to the wild-type:kainate complex involves a twisting motion with the efficacy contribution opposite from that expected based on previous analyses. As a result, channel opening may involve transmembrane rearrangements with a significant rotational component. Furthermore, a two-dimensional analysis of agonist-induced GluA2 LBD motions suggests that efficacy is not a linearly varying function of lobe 2 displacement vectors, but is rather determined by specific conformational requirements of the transmembrane domains.


    Organizational Affiliation

    Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire 03755, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 4
A
257Rattus norvegicusMutation(s): 1 
Gene Names: Glur4Gria4
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:  1980   nM  BindingDB
KAIKi:  8050   nM  BindingDB
KAIEC50:  73000   nM  BindingDB
KAIEC50:  26610   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
KAIKi:  1710   nM  BindingDB
KAIKi:  1714   nM  BindingDB
KAIKi:  3690   nM  BindingDB
KAIKi:  1.7999999523162842   nM  BindingDB
KAIEC50:  10570   nM  BindingDB
KAIKi:  6300   nM  BindingDB
KAIKi:  12200   nM  BindingDB
KAIKi:  12221   nM  BindingDB
KAIEC50:  40000   nM  BindingDB
KAIKi:  3570   nM  BindingDB
KAIEC50:  31000   nM  BindingDB
KAIEC50:  47000   nM  BindingDB
KAIEC50:  7510   nM  BindingDB
KAIKi:  5780   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.190 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.69α = 90
b = 48.445β = 106.62
c = 62.834γ = 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: 2009-10-27 
  • Released Date: 2010-02-09 
  • Deposition Author(s): Gill, A., Madden, D.R.

Revision History 

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-02
    Changes: Advisory, Refinement description, Source and taxonomy
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description