2AL5

Crystal structure of the GluR2 ligand binding core (S1S2J) in complex with fluoro-willardiine and aniracetam


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanism of positive allosteric modulators acting on AMPA receptors.

Jin, R.Clark, S.Weeks, A.M.Dudman, J.T.Gouaux, E.Partin, K.M.

(2005) J.Neurosci. 25: 9027-9036

  • DOI: 10.1523/JNEUROSCI.2567-05.2005
  • Primary Citation of Related Structures:  
  • Also Cited By: 4IY6, 4IY5

  • PubMed Abstract: 
  • Ligand-gated ion channels involved in the modulation of synaptic strength are the AMPA, kainate, and NMDA glutamate receptors. Small molecules that potentiate AMPA receptor currents relieve cognitive deficits caused by neurodegenerative diseases such ...

    Ligand-gated ion channels involved in the modulation of synaptic strength are the AMPA, kainate, and NMDA glutamate receptors. Small molecules that potentiate AMPA receptor currents relieve cognitive deficits caused by neurodegenerative diseases such as Alzheimer's disease and show promise in the treatment of depression. Previously, there has been limited understanding of the molecular mechanism of action for AMPA receptor potentiators. Here we present cocrystal structures of the glutamate receptor GluR2 S1S2 ligand-binding domain in complex with aniracetam [1-(4-methoxybenzoyl)-2-pyrrolidinone] or CX614 (pyrrolidino-1,3-oxazino benzo-1,4-dioxan-10-one), two AMPA receptor potentiators that preferentially slow AMPA receptor deactivation. Both potentiators bind within the dimer interface of the nondesensitized receptor at a common site located on the twofold axis of molecular symmetry. Importantly, the potentiator binding site is adjacent to the "hinge" in the ligand-binding core "clamshell" that undergoes conformational rearrangement after glutamate binding. Using rapid solution exchange, patch-clamp electrophysiology experiments, we show that point mutations of residues that interact with potentiators in the cocrystal disrupt potentiator function. We suggest that the potentiators slow deactivation by stabilizing the clamshell in its closed-cleft, glutamate-bound conformation.


    Related Citations: 
    • Structural basis for partial agonist action at ionotropic glutamate receptors.
      Jin, R.,Banke, T.G.,Mayer, M.L.,Traynelis, S.F.,Gouaux, E.
      (2003) NAT.NEUROSCI. 6: 803
    • Mechanism of glutamate receptor desensitization.
      Sun, Y.,Olson, R.,Horning, M.,Armstrong, N.,Mayer, M.,Gouaux, E.
      (2002) Nature 417: 245


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
A, B
263Rattus norvegicusMutation(s): 0 
Gene Names: Gria2 (Glur2)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4MP
Query on 4MP

Download SDF File 
Download CCD File 
A
1-(4-METHOXYBENZOYL)-2-PYRROLIDINONE
ANIRACETAM, 1-P-ANISOYL-2-PYRROLIDINONE
C12 H13 N O3
ZXNRTKGTQJPIJK-UHFFFAOYSA-N
 Ligand Interaction
FWD
Query on FWD

Download SDF File 
Download CCD File 
A, B
2-AMINO-3-(5-FLUORO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID
FLUORO-WILLARDIINE
C7 H8 F N3 O4
DBWPFHJYSTVBCZ-BYPYZUCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FWDEC50: 460 - 20900 nM (99) BINDINGDB
FWDKi: 4 - >10000 nM (99) BINDINGDB
FWDKi: 4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.056α = 90.00
b = 64.126β = 90.07
c = 107.949γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-08-02
    Type: Source and taxonomy