Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.71 kDa 
• Atom Count: 4509 
• Residue Count: 497 
• Unique protein chains: 1

2XXV

Crystal structure of the GluK2 (GluR6) M770K LBD dimer in complex with kainate

• DOI: 10.2210/pdb2XXV/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-11-12 Released: 2011-02-09 
• Deposition Author(s): Nayeem, N., Mayans, O., Green, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.203 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Literature

Conformational Flexibility of the Ligand-Binding Domain Dimer in Kainate Receptor Gating and Desensitization

Nayeem, N., Mayans, O., Green, T.

(2011) J Neurosci 31: 2916

• PubMed: 21414913 
• DOI: 10.1523/JNEUROSCI.4771-10.2011
• Primary Citation of Related Structures:  
  2XXR, 2XXT, 2XXU, 2XXV, 2XXW, 2XXX, 2XXY


• PubMed Abstract: 
  

AMPA- and kainate (KA)-selective ionotropic glutamate receptors (iGluRs) respond to agonist by opening (gating), then closing (desensitizing) in quick succession. Gating has been linked to agonist-induced changes within the ligand-binding domain (LBD), and desensitization to rearrangement of a dimer formed by neighboring LBDs. To explore the role of dimer conformation in both gating and desensitization, we compared the conformational effects of two kainate receptor mutants. The first, GluK2-D776K, blocks desensitization of macroscopic current responses ("macroscopic desensitization"). The second, GluK2-M770K, accelerates macroscopic desensitization and eliminates the effects of external ions on channel kinetics. Using structures determined by x-ray crystallography, we found that in both mutants the introduced lysines act as tethered cations, displacing sodium ions from their binding sites within the dimer interface. This results in new inter- and intra-protomer contacts in D776K and M770K respectively, explaining the effects of these mutations on dimer stability and desensitization kinetics. Further, chloride binding was unaffected by the M770K mutation, even though binding of sodium ions has been proposed to promote dimer stability by stabilizing anion binding. This suggests sodium binding may affect receptor function more directly than currently supposed. Notably, we also observed a ligand-specific shift in dimer conformation when comparing LBD dimers in complex with glutamate or the partial agonist KA, revealing a previously unidentified role for dimer orientation in iGluR gating.

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Organizational Affiliation: 

Department of Pharmacology, University of Liverpool, Liverpool L69 3BX, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2	A, B	261	Rattus norvegicus	Mutation(s): 1  Gene Names: Grik2, Glur6
Find proteins for P42260 (Rattus norvegicus) Explore P42260  Go to UniProtKB:  P42260

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KAI	A, B	3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE C10 H15 N O4 VLSMHEGGTFMBBZ-OOZYFLPDSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
KAI	EC50:  1800   nM  BindingDB
KAI	Ki:  1.409999966621399   nM  BindingDB
KAI	Ki:  3.700000047683716   nM  BindingDB
KAI	Kd:  39   nM  BindingDB
KAI	EC50:  700   nM  BindingDB
KAI	Ki:  53   nM  BindingDB
KAI	Ki:  32   nM  BindingDB
KAI	Ki:  12.699999809265137   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.203 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.26	α = 90
b = 104.873	β = 90
c = 113.589	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-11-12 
• Released Date: 2011-02-09 
Deposition Author(s): Nayeem, N., Mayans, O., Green, T.

Revision History 

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2012-04-04
  Changes: Database references, Refinement description, Version format compliance
• Version 1.2: 2019-01-30
  Changes: Data collection, Experimental preparation, Other