3RT8

Chlorowillardiine bound to the ligand binding domain of GluA3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.426 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanisms of Modal Activation of GluA3 Receptors.

Poon, K.Ahmed, A.H.Nowak, L.M.Oswald, R.E.

(2011) Mol.Pharmacol. 80: 49-59

  • DOI: 10.1124/mol.111.071688
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • AMPA receptors are the major excitatory neurotransmitter receptors in the central nervous system and are involved in numerous neurological disorders. An agonist-binding site is present in each of four subunits that form a functional channel. Binding ...

    AMPA receptors are the major excitatory neurotransmitter receptors in the central nervous system and are involved in numerous neurological disorders. An agonist-binding site is present in each of four subunits that form a functional channel. Binding consists of three steps: docking of agonist to the bilobed ligand binding domain (LBD), closure of the LBD, and increased stability of the closed-lobe conformation through interlobe hydrogen bonding. We describe GluA3 single channel currents activated by nitrowillardiine (NO(2)W) and chlorowillardiine (ClW) in the presence of cyclothiazide, in conjunction with crystal structures of GluA2 and GluA3 LBDs bound to fluorowillardiine (FW), ClW, and NO(2)W. When bound to NO(2)W or ClW, the GluA3 channel opens to three conductance levels with comparable open probabilities and displays modal behavior similar to that obtained with glutamate and FW as agonists (Poon et al., 2010). At lower concentrations, ClW evoked an alternate kinetic behavior, consisting of high open probability in lower conductance states. The structure of ClW bound to GluA3 LBD exhibits a unique partially open hydrogen bonding structure that may be associated with these alternative kinetics. NO(2)W evoked longer open times than seen for other agonists in high and very high modes. The structure ofGluA2 LBD bound to NO(2)W exhibits fully closed lobes with additional interlobe interactions mediated by the nitro group. Beyond differences in efficacy between full and partial agonists, the complexities of the single channel behavior of AMPA receptors may also be associated with small interactions that modify the stability of various degrees of closure.


    Organizational Affiliation

    Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 3
A
258Rattus norvegicusMutation(s): 0 
Gene Names: Gria3 (Glur3)
Find proteins for P19492 (Rattus norvegicus)
Go to UniProtKB:  P19492
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CWD
Query on CWD

Download SDF File 
Download CCD File 
A
3-(5-chloro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine
chlorowillardiine
C7 H8 Cl N3 O4
HEHLSRRDKJVHOM-BYPYZUCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CWDKi: 45 - 561 nM (88) BINDINGDB
CWDEC50: 2110 nM (88) BINDINGDB
CWDKi: 451 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.426 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.223 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 49.325α = 90.00
b = 49.157β = 90.00
c = 140.478γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-07-26
    Type: Data collection, Source and taxonomy