3H6U

Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and NS1493 at 1.85 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Distinct structural features of cyclothiazide are responsible for effects on peak current amplitude and desensitization kinetics at iGluR2.

Hald, H.Ahring, P.K.Timmermann, D.B.Liljefors, T.Gajhede, M.Kastrup, J.S.

(2009) J.Mol.Biol. 391: 906-917

  • DOI: 10.1016/j.jmb.2009.07.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ionotropic glutamate receptors (iGluRs) mediate fast excitatory neurotransmission. Upon glutamate application, 2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid receptors undergo rapid and almost complete desensitization that can be attenuate ...

    Ionotropic glutamate receptors (iGluRs) mediate fast excitatory neurotransmission. Upon glutamate application, 2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid receptors undergo rapid and almost complete desensitization that can be attenuated by positive allosteric modulators. The molecular mechanism of positive allosteric modulation has been elucidated previously by crystal structures of the ligand-binding core of iGluR2 in complex with, for example, cyclothiazide (CTZ). Here, we investigate the structure and function of CTZ and three closely related analogues NS1493, NS5206, and NS5217 at iGluR2, by X-ray crystallography and fast application patch-clamp electrophysiology. CTZ was the most efficacious and potent modulator of the four compounds on iGluR2(Q)(i) [E(max) normalized to response of glutamate: 754% (CTZ), 490% (NS1493), 399% (NS5206), and 476% (NS5217) and EC(50) in micromolar: 10 (CTZ), 26 (NS1493), 43 (NS5206), and 48 (NS5217)]. The four modulators divide into three groups according to efficacy and desensitization kinetics: (1) CTZ increases the peak current efficacy twice as much as the three analogues and nearly completely blocks receptor desensitization; (2) NS5206 and NS5217 have low efficacy and only attenuate desensitization partially; (3) NS1493 has low efficacy but nearly completely blocks receptor desensitization. A hydrophobic substituent at the 3-position of the 1,1-dioxo-3,4-dihydro-2H-benzo[e][1,2,4]thiadiazine ring system is important for compound efficacy, with the following ranking: norbornenyl (bicyclo[2.2.1]hept-2-ene)>cyclopentyl>methyl. The replacement of the norbornenyl moiety with a significantly less hydrophobic cyclopentane ring increases the flexibility of the modulator as the cyclopentane ring adopts various conformations at the iGluR2 allosteric binding site. The main structural feature responsible for a nearly complete block of desensitization is the presence of an NH hydrogen bond donor in the 4-position of the 1,1-dioxo-3,4-dihydro-2H-benzo[e][1,2,4]thiadiazine ring system, forming an anchoring hydrogen bond to Ser754. Therefore, the atom at the 4-position of CTZ seems to be a major determinant of receptor desensitization kinetics.


    Related Citations: 
    • Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: crystal structures of the GluR2 ligand binding core.
      Armstrong, N.,Gouaux, E.
      (2000) Neuron 28: 165
    • 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 Medicinal Chemistry, University of Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
A
263Rattus norvegicusMutation(s): 1 
Gene Names: Gria2 (Glur2)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NS3
Query on NS3

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Download CCD File 
A
(3S)-3-cyclopentyl-6-methyl-7-[(4-methylpiperazin-1-yl)sulfonyl]-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide
C18 H28 N4 O4 S2
CUMKMTBOHBENJI-SFHVURJKSA-N
 Ligand Interaction
GLU
Query on GLU

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Download CCD File 
A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
FLC
Query on FLC

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Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 88.462α = 90.00
b = 64.086β = 90.00
c = 47.272γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
CNSrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-08-02
    Type: Source and taxonomy
  • Version 1.3: 2017-11-01
    Type: Refinement description