4BDR

Crystal structure of the GluK2 R775A LBD dimer in complex with kainate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Correlating Efficacy and Desensitization with Gluk2 Ligand-Binding Domain Movements.

Nayeem, N.Mayans, O.Green, T.

(2013) Open Biol. 3: 0051

  • DOI: 10.1098/rsob.130051
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Gating of AMPA- and kainate-selective ionotropic glutamate receptors can be defined in terms of ligand affinity, efficacy and the rate and extent of desensitization. Crucial insights into all three elements have come from structural studies of the li ...

    Gating of AMPA- and kainate-selective ionotropic glutamate receptors can be defined in terms of ligand affinity, efficacy and the rate and extent of desensitization. Crucial insights into all three elements have come from structural studies of the ligand-binding domain (LBD). In particular, binding-cleft closure is associated with efficacy, whereas dissociation of the dimer formed by neighbouring LBDs is linked with desensitization. We have explored these relationships in the kainate-selective subunit GluK2 by studying the effects of mutating two residues (K531 and R775) that form key contacts within the LBD dimer interface, but whose truncation unexpectedly attenuates desensitization. One mutation (K531A) also switches the relative efficacies of glutamate and kainate. LBD crystal structures incorporating these mutations revealed several conformational changes that together explain their phenotypes. K531 truncation results in new dimer contacts, consistent with slower desensitization and sideways movement in the ligand-binding cleft correlating with efficacy. The tested mutants also disrupted anion binding; no chloride was detected in the dimer-interface site, including in R775A where absence of chloride was the only structural change evident. From this, we propose that the charge balance in the GluK2 LBD dimer interface maintains a degree of instability, necessary for rapid and complete desensitization.


    Organizational Affiliation

    Department of Pharmacology, University of Liverpool, Liverpool L69 3GE, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
A, B
261Rattus norvegicusMutation(s): 1 
Gene Names: Grik2 (Glur6)
Find proteins for P42260 (Rattus norvegicus)
Go to UniProtKB:  P42260
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
KAI
Query on KAI

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Download CCD File 
A, B
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE
KAINATE
C10 H15 N O4
VLSMHEGGTFMBBZ-OOZYFLPDSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KAIEC50: 1800 nM (97) BINDINGDB
KAIKi: 3.7 - 12.7 nM (97) BINDINGDB
KAIKd: 39 nM (97) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.164 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 95.503α = 90.00
b = 105.331β = 90.00
c = 112.179γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-06-12
    Type: Database references
  • Version 1.2: 2015-04-29
    Type: Data collection, Source and taxonomy
  • Version 2.0: 2018-06-20
    Type: Atomic model, Data collection, Derived calculations