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: 59.42 kDa 
• Atom Count: 4458 
• Residue Count: 499 
• Unique protein chains: 1

4BDQ

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

• DOI: 10.2210/pdb4BDQ/pdb

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


• Deposited: 2012-10-05 Released: 2013-04-10 
• Deposition Author(s): Nayeem, N., Mayans, O., Green, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.213 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

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

Nayeem, N., Mayans, O., Green, T.

(2013) Open Biol 3: 0051

• PubMed: 23720540 
• DOI: 10.1098/rsob.130051
• Primary Citation of Related Structures:  
  4BDN, 4BDO, 4BDQ, 4BDR, 4BDL, 4BDM


• 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 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.

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Organizational Affiliation: 

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

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
GLU	A, B	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
NA	A, B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.213 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.753	α = 90
b = 105.585	β = 90
c = 114.608	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: 2012-10-05 
• Released Date: 2013-04-10 
Deposition Author(s): Nayeem, N., Mayans, O., Green, T.

Revision History 

• Version 1.0: 2013-04-10
  Type: Initial release
  
• Version 1.1: 2013-06-12
  Changes: Database references
• Version 1.2: 2015-04-29
  Changes: Data collection