3H03

Crystal structure of the binding domain of the AMPA subunit GluR2 bound to UBP277


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanisms of antagonism of the GluR2 AMPA receptor: structure and dynamics of the complex of two willardiine antagonists with the glutamate binding domain.

Ahmed, A.H.Thompson, M.D.Fenwick, M.K.Romero, B.Loh, A.P.Jane, D.E.Sondermann, H.Oswald, R.E.

(2009) Biochemistry 48: 3894-3903

  • DOI: 10.1021/bi900107m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ionotropic glutamate receptors mediate the majority of vertebrate excitatory synaptic transmission. The development of selective antagonists for glutamate receptor subtypes is of interest in the treatment of a variety of neurological disorders. This ...

    Ionotropic glutamate receptors mediate the majority of vertebrate excitatory synaptic transmission. The development of selective antagonists for glutamate receptor subtypes is of interest in the treatment of a variety of neurological disorders. This study presents the crystal structure of the binding domain of GluR2 bound to two antagonists (UBP277 and UBP282) that are derivatives of the natural product, willardiine. The antagonists bind to one lobe of the protein with interactions similar to agonists. Interaction with the second lobe differs between the two antagonists, resulting in a different position of the uracil ring and different orientations of the bilobed structure. UBP277 binding produces a stable lobe orientation that is similar to the apo state, but the binding of UBP282 produces the largest hyperextension of the lobes yet reported for an AMPA receptor. The carboxyethyl (UBP277) and carboxybenzyl (UBP282) substituents in the N(3) position keep the lobes separated by a "foot-in-the-door" mechanism and the internal dynamics are minimal compared to the CNQX-bound form of the protein (which makes minimal contacts with one of the two lobes). In contrast to the antagonists CNQX and DNQX, UBP277 and UBP282 produce complexes with higher thermal stability, but affinities that are more than 100-fold lower. These structures support the idea that antagonism is associated with the overall orientation of the lobes rather than with specific interactions, and antagonism can rise either from specific interactions with both lobes ("foot-in-the-door" mechanism) or from the lack of extensive interactions with one of the two lobes.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
A, B, D, G
258Rattus 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
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, D, G
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UBP
Query on UBP

Download SDF File 
Download CCD File 
A, B, D, G
3-[3-(2-carboxyethyl)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl]-L-alanine
(S)-1-(2-amino-2-carboxyethyl)-3-(2-carboxyethyl)pyrimidine-2,4-dione
C10 H13 N3 O6
CNWDQZBURPNJRN-LURJTMIESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UBPIC50: 135000 nM BINDINGMOAD
UBPIC50: 135000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 98.953α = 90.00
b = 57.719β = 114.88
c = 105.461γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data collection
PHENIXmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-08-23
    Type: Data collection, Source and taxonomy
  • Version 1.3: 2018-06-27
    Type: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary