2ZNS

Crystal structure of the ligand-binding core of the human ionotropic glutamate receptor, GluR5, in complex with glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Binding and Selectivity of the Marine Toxin Neodysiherbaine A and Its Synthetic Analogues to GluK1 and GluK2 Kainate Receptors.

Unno, M.Shinohara, M.Takayama, K.Tanaka, H.Teruya, K.Doh-Ura, K.Sakai, R.Sasaki, M.Ikeda-Saito, M.

(2011) J.Mol.Biol. 413: 667-683

  • DOI: 10.1016/j.jmb.2011.08.043
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dysiherbaine (DH) and neodysiherbaine A (NDH) selectively bind and activate two kainate-type ionotropic glutamate receptors, GluK1 and GluK2. The ligand-binding domains of human GluK1 and GluK2 were crystallized as bound forms with a series of DH ana ...

    Dysiherbaine (DH) and neodysiherbaine A (NDH) selectively bind and activate two kainate-type ionotropic glutamate receptors, GluK1 and GluK2. The ligand-binding domains of human GluK1 and GluK2 were crystallized as bound forms with a series of DH analogues including DH, NDH, 8-deoxy-NDH, 9-deoxy-NDH and 8,9-dideoxy-NDH (MSVIII-19), isolated from natural sources or prepared by total synthesis. Since the DH analogues exhibit a wide range of binding affinities and agonist efficacies, it follows that the detailed analysis of crystal structure would provide us with a significant opportunity to elucidate structural factors responsible for selective binding and some aspects of gating efficacy. We found that differences in three amino acids (Thr503, Ser706 and Ser726 in GluK1 and Ala487, Asn690 and Thr710 in GluK2) in the ligand-binding pocket generate differences in the binding modes of NDH to GluK1 and GluK2. Furthermore, deletion of the C(9) hydroxy group in NDH alters the ligand conformation such that it is no longer suited for binding to the GluK1 ligand-binding pocket. In GluK2, NDH pushes and rotates the side chain of Asn690 (substituted for Ser706 in GluK1) and disrupts an interdomain hydrogen bond with Glu409. The present data support the idea that receptor selectivities of DH analogues resulted from the differences in the binding modes of the ligands in GluK1/GluK2 and the steric repulsion of Asn690 in GluK2. All ligands, regardless of agonist efficacy, induced full domain closure. Consequently, ligand efficacy and domain closure did not directly coincide with DH analogues and the kainate receptors.


    Organizational Affiliation

    Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Naka, Ibaraki 319-1106, Japan. unno19@mx.ibaraki.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor, ionotropic kainate 1
A
256Homo sapiensMutation(s): 0 
Gene Names: GRIK1 (GLUR5)
Find proteins for P39086 (Homo sapiens)
Go to Gene View: GRIK1
Go to UniProtKB:  P39086
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

Download SDF File 
Download CCD File 
A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GLUKi: 290 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 119.391α = 90.00
b = 63.576β = 106.73
c = 50.147γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
ADSCdata collection
REFMACrefinement
CNSphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-10-26
    Type: Database references
  • Version 1.3: 2017-08-16
    Type: Source and taxonomy