1II5

CRYSTAL STRUCTURE OF THE GLUR0 LIGAND BINDING CORE COMPLEX WITH L-GLUTAMATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Mechanisms for ligand binding to GluR0 ion channels: crystal structures of the glutamate and serine complexes and a closed apo state.

Mayer, M.L.Olson, R.Gouaux, E.

(2001) J Mol Biol 311: 815-836

  • DOI: 10.1006/jmbi.2001.4884
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • High-resolution structures of the ligand binding core of GluR0, a glutamate receptor ion channel from Synechocystis PCC 6803, have been solved by X-ray diffraction. The GluR0 structures reveal homology with bacterial periplasmic binding proteins and ...

    High-resolution structures of the ligand binding core of GluR0, a glutamate receptor ion channel from Synechocystis PCC 6803, have been solved by X-ray diffraction. The GluR0 structures reveal homology with bacterial periplasmic binding proteins and the rat GluR2 AMPA subtype neurotransmitter receptor. The ligand binding site is formed by a cleft between two globular alpha/beta domains. L-Glutamate binds in an extended conformation, similar to that observed for glutamine binding protein (GlnBP). However, the L-glutamate gamma-carboxyl group interacts exclusively with Asn51 in domain 1, different from the interactions of ligand with domain 2 residues observed for GluR2 and GlnBP. To address how neutral amino acids activate GluR0 gating we solved the structure of the binding site complex with L-serine. This revealed solvent molecules acting as surrogate ligand atoms, such that the serine OH group makes solvent-mediated hydrogen bonds with Asn51. The structure of a ligand-free, closed-cleft conformation revealed an extensive hydrogen bond network mediated by solvent molecules. Equilibrium centrifugation analysis revealed dimerization of the GluR0 ligand binding core with a dissociation constant of 0.8 microM. In the crystal, a symmetrical dimer involving residues in domain 1 occurs along a crystallographic 2-fold axis and suggests that tetrameric glutamate receptor ion channels are assembled from dimers of dimers. We propose that ligand-induced conformational changes cause the ion channel to open as a result of an increase in domain 2 separation relative to the dimer interface.


    Related Citations: 
    • FUNCTIONAL CHARACTERIZATION OF A POTASSIUM-SELECTIVE PROKARYOTIC GLUTAMATE RECEPTOR
      CHEN, G.-Q., CUI, C., MAYER, M.L., GOUAUX, E.
      (1999) Nature 402: 817

    Organizational Affiliation

    Laboratory of Cellular and MolecularNeurophysiology, National Institute of Child Health and Human Development, National Institutes of Health, Building 49, Room 5A78, 49 Convent Drive MSC 4495, Bethesda, MD 20892, USA. mlm@helix.nih.gov



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Slr1257 proteinA233Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: GluR0 slr1257slr1257
Find proteins for P73797 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore P73797 
Go to UniProtKB:  P73797
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

Download CCD File 
A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GLUKd :  240   nM  PDBBind
GLUKd:  240   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.866α = 90
b = 49.706β = 116.84
c = 55.572γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-04-11
    Changes: Database references
  • Version 1.4: 2017-08-02
    Changes: Refinement description, Source and taxonomy