3H6G

Crystal structure of the GluR6 amino terminal domain dimer assembly


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.697 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The N-terminal domain of GluR6-subtype glutamate receptor ion channels.

Kumar, J.Schuck, P.Jin, R.Mayer, M.L.

(2009) Nat.Struct.Mol.Biol. 16: 631-638

  • DOI: 10.1038/nsmb.1613
  • Primary Citation of Related Structures:  3H6H

  • PubMed Abstract: 
  • The amino-terminal domain (ATD) of glutamate receptor ion channels, which controls their selective assembly into AMPA, kainate and NMDA receptor subtypes, is also the site of action of NMDA receptor allosteric modulators. Here we report the crystal s ...

    The amino-terminal domain (ATD) of glutamate receptor ion channels, which controls their selective assembly into AMPA, kainate and NMDA receptor subtypes, is also the site of action of NMDA receptor allosteric modulators. Here we report the crystal structure of the ATD from the kainate receptor GluR6. The ATD forms dimers in solution at micromolar protein concentrations and crystallizes as a dimer. Unexpectedly, each subunit adopts an intermediate extent of domain closure compared to the apo and ligand-bound complexes of LIVBP and G protein-coupled glutamate receptors (mGluRs), and the dimer assembly has a markedly different conformation from that found in mGluRs. This conformation is stabilized by contacts between large hydrophobic patches in the R2 domain that are absent in NMDA receptors, suggesting that the ATDs of individual glutamate receptor ion channels have evolved into functionally distinct families.


    Organizational Affiliation

    Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, Bethesda, Maryland, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor, ionotropic kainate 2
A, B
395Rattus norvegicusGene Names: Grik2 (Glur6)
Find proteins for P42260 (Rattus norvegicus)
Go to UniProtKB:  P42260
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
TLA
Query on TLA

Download SDF File 
Download CCD File 
A, B
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.697 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 172.074α = 90.00
b = 172.074β = 90.00
c = 111.547γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
PHENIXrefinement
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-04-23 
  • Released Date: 2009-05-26 
  • Deposition Author(s): Kumar, J., Mayer, M.L.

Revision History 

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance