4F39

Kainate bound to the ligand binding domain of GluA3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The loss of an electrostatic contact unique to AMPA receptor ligand binding domain 2 slows channel activation.

Holley, S.M.Ahmed, A.H.Srinivasan, J.Murthy, S.E.Weiland, G.A.Oswald, R.E.Nowak, L.M.

(2012) Biochemistry 51: 4015-4027

  • DOI: 10.1021/bi3001837
  • Primary Citation of Related Structures:  
    4F1Y, 4F22, 4F29, 4F2O, 4F2Q, 4F31, 4F39, 4F3B, 4F3G

  • PubMed Abstract: 
  • Ligand-gated ion channels undergo conformational changes that transfer the energy of agonist binding to channel opening. Within ionotropic glutamate receptor (iGluR) subunits, this process is initiated in their bilobate ligand binding domain (LBD) where agonist binding to lobe 1 favors closure of lobe 2 around the agonist and allows formation of interlobe hydrogen bonds ...

    Ligand-gated ion channels undergo conformational changes that transfer the energy of agonist binding to channel opening. Within ionotropic glutamate receptor (iGluR) subunits, this process is initiated in their bilobate ligand binding domain (LBD) where agonist binding to lobe 1 favors closure of lobe 2 around the agonist and allows formation of interlobe hydrogen bonds. AMPA receptors (GluAs) differ from other iGluRs because glutamate binding causes an aspartate-serine peptide bond in a flexible part of lobe 2 to rotate 180° (flipped conformation), allowing these residues to form cross-cleft H-bonds with tyrosine and glycine in lobe 1. This aspartate also contacts the side chain of a lysine residue in the hydrophobic core of lobe 2 by a salt bridge. We investigated how the peptide flip and electrostatic contact (D655-K660) in GluA3 contribute to receptor function by examining pharmacological and structural properties with an antagonist (CNQX), a partial agonist (kainate), and two full agonists (glutamate and quisqualate) in the wildtype and two mutant receptors. Alanine substitution decreased the agonist potency of GluA3(i)-D655A and GluA3(i)-K660A receptor channels expressed in HEK293 cells and differentially affected agonist binding affinity for isolated LBDs without changing CNQX affinity. Correlations observed in the crystal structures of the mutant LBDs included the loss of the D655-K660 electrostatic contact, agonist-dependent differences in lobe 1 and lobe 2 closure, and unflipped D(A)655-S656 bonds. Glutamate-stimulated activation was slower for both mutants, suggesting that efficient energy transfer of agonist binding within the LBD of AMPA receptors requires an intact tether between the flexible peptide flip domain and the rigid hydrophobic core of lobe 2.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 3A258Rattus norvegicusMutation(s): 0 
Gene Names: Glur3Gria3
UniProt
Find proteins for P19492 (Rattus norvegicus)
Explore P19492 
Go to UniProtKB:  P19492
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KAI (Subject of Investigation/LOI)
Query on KAI

Download Ideal Coordinates CCD File 
B [auth A]3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE
C10 H15 N O4
VLSMHEGGTFMBBZ-OOZYFLPDSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
KAI BindingDB:  4F39 Ki: min: 1.8, max: 1.22e+4 (nM) from 15 assay(s)
EC50: min: 7510, max: 3.80e+5 (nM) from 9 assay(s)
PDBBind:  4F39 Ki: 1980 (nM) from 1 assay(s)
Binding MOAD:  4F39 Ki: 3440 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.09α = 90
b = 57.565β = 90
c = 115.336γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHENIXmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2012-06-20
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Data collection, Source and taxonomy