5NG9

Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist CIP-AS at 1.15 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.109 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and Affinity of Two Bicyclic Glutamate Analogues at AMPA and Kainate Receptors.

Mllerud, S.Pinto, A.Marconi, L.Frydenvang, K.Thorsen, T.S.Laulumaa, S.Venskutonyte, R.Winther, S.Moral, A.M.C.Tamborini, L.Conti, P.Pickering, D.S.Kastrup, J.S.

(2017) ACS Chem Neurosci 8: 2056-2064

  • DOI: 10.1021/acschemneuro.7b00201
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ionotropic glutamate receptors (iGluRs) are involved in most of the fast excitatory synaptic transmission in the central nervous system. These receptors are important for learning and memory formation, but are also involved in the development of dise ...

    Ionotropic glutamate receptors (iGluRs) are involved in most of the fast excitatory synaptic transmission in the central nervous system. These receptors are important for learning and memory formation, but are also involved in the development of diseases such as Alzheimer's disease, epilepsy and depression. To understand the function of different types of iGluRs, selective agonists are invaluable as pharmacological tool compounds. Here, we report binding affinities of two bicyclic, conformationally restricted analogues of glutamate (CIP-AS and LM-12b) at AMPA (GluA2 and GluA3) and kainate receptor subunits (GluK1-3 and GluK5). Both CIP-AS and LM-12b were found to be GluK3-preferring agonists, with Ki of 6 and 22 nM, respectively, at recombinant GluK3 receptors. The detailed binding mode of CIP-AS and LM-12b in the ligand-binding domains of the AMPA receptor subunit GluA2 (GluA2-LBD) and the kainate receptor subunits GluK1 (GluK1-LBD) and GluK3 (GluK3-LBD) was investigated by X-ray crystallography. CIP-AS stabilized all three receptor constructs in conformations similar to those with kainate. Remarkably, whereas LM-12b bound in a similar manner to CIP-AS in GluA2-LBD and GluK3-LBD, it introduced full closure of the ligand-binding domain in GluK1-LBD and formation of a D1-D2 interlobe hydrogen bond between Glu441 and Ser721, as also observed with glutamate. As the binding affinity of LM-12b at GluK1 is ∼8-fold better than that for CIP-AS (Ki of 85 and 656 nM, respectively), it shows that small changes in agonist structure can lead to prominent differences in structure and function.


    Organizational Affiliation

    Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen , 2100 Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
A
264Rattus norvegicusMutation(s): 0 
Gene Names: Gria2 (Glur2)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8VN
Query on 8VN

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A
(3~{a}~{S},4~{S},6~{a}~{R})-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-d][1,2]oxazole-3,4-dicarboxylic acid
C7 H8 N2 O5
JMTZNIDIUDLCMK-HZLVTQRSSA-N
 Ligand Interaction
8WQ
Query on 8WQ

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A
(2~{S},3~{R},4~{R})-3-(carboxycarbonyl)-4-oxidanyl-pyrrolidine-2-carboxylic acid
C7 H9 N O6
XAWWSRPWEJXFEU-HZLVTQRSSA-N
 Ligand Interaction
LI
Query on LI

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A
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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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
FLC
Query on FLC

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.109 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 62.218α = 90.00
b = 88.140β = 90.00
c = 47.958γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Database references