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: 59.29 kDa 
• Atom Count: 4887 
• Residue Count: 505 
• Unique protein chains: 1

3G3F

Crystal structure of the GluR6 ligand binding domain dimer with glutamate and NaCl at 1.38 Angstrom resolution

• DOI: 10.2210/pdb3G3F/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-02 Released: 2009-06-02 
• Deposition Author(s): Chaudhry, C., Mayer, M.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.175 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 

Literature

Stability of ligand-binding domain dimer assembly controls kainate receptor desensitization.

Chaudhry, C., Weston, M.C., Schuck, P., Rosenmund, C., Mayer, M.L.

(2009) EMBO J 28: 1518-1530

• PubMed: 19339989 
• DOI: 10.1038/emboj.2009.86
• Primary Citation of Related Structures:  
  3G3G, 3G3H, 3G3I, 3G3J, 3G3K, 3G3F


• PubMed Abstract: 
  

AMPA and kainate receptors mediate fast synaptic transmission. AMPA receptor ligand-binding domains form dimers, which are key functional units controlling ion-channel activation and desensitization. Dimer stability is inversely related to the rate and extent of desensitization. Kainate and AMPA receptors share common structural elements, but functional measurements suggest that subunit assembly and gating differs between these subtypes. To investigate this, we constructed a library of GluR6 kainate receptor mutants and directly measured changes in kainate receptor dimer stability by analytical ultracentrifugation, which, combined with electrophysiological experiments, revealed an inverse correlation between dimer stability and the rate of desensitization. We solved crystal structures for a series of five GluR6 mutants, to understand the molecular mechanisms for dimer stabilization. We demonstrate that the desensitized state of kainate receptors acts as a deep energy well offsetting the stabilizing effects of dimer interface mutants, and that the deactivation of kainate receptor responses is dominated by entry into desensitized states. Our results show how neurotransmitter receptors with similar structures and gating mechanisms can exhibit strikingly different functional properties.

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Organizational Affiliation: 

Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, NICHD, NIH, DHHS, Bethesda, MD, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor, ionotropic kainate 2	A, B	259	Rattus norvegicus	Mutation(s): 0  Gene Names: Glur6, Grik2
Find proteins for P42260 (Rattus norvegicus) Explore P42260  Go to UniProtKB:  P42260

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLU	A, B	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
IPA	A, B	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	A, B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
GGL	Ki:  330   nM  BindingDB
GGL	Ki:  331   nM  BindingDB
GGL	Ki:  332   nM  BindingDB
GGL	EC50:  25000   nM  BindingDB
GGL	EC50:  73000   nM  BindingDB
GGL	Ki:  1106   nM  BindingDB
GGL	EC50:  66000   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.175 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.185	α = 90
b = 114.153	β = 115.31
c = 52.364	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-02 
• Released Date: 2009-06-02 
Deposition Author(s): Chaudhry, C., Mayer, M.L.

Revision History 

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-07-26
  Changes: Refinement description, Source and taxonomy