PDBsum entry 2ojt

Membrane protein

PDB id: 2ojt

Contents

Protein chains

251 a.a. *

Ligands

1PE ×2

UBA ×2

Metals

_BR ×2

Waters ×288

* Residue conservation analysis

PDB id:

2ojt

Name:

Membrane protein

Title:

Structure and mechanism of kainate receptor modulation by anions

Structure:

Glutamate receptor, ionotropic kainate 1. Chain: a, b. Synonym: glutamate receptor 5, glur-5, glur5. Engineered: yes. Mutation: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Tissue: brain. Gene: grik1, glur5. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.95Å R-factor: 0.192 R-free: 0.233

Authors:

M.L.Mayer

Key ref:

A.J.Plested and M.L.Mayer (2007). Structure and mechanism of kainate receptor modulation by anions. Neuron, 53, 829-841. PubMed id: 17359918 DOI: 10.1016/j.neuron.2007.02.025

Date:

14-Jan-07 Release date: 03-Apr-07

Protein chains

P22756  (GRIK1_RAT) -  Glutamate receptor ionotropic, kainate 1 from Rattus norvegicus

Seq: 949 a.a.

Struc: 251 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1016/j.neuron.2007.02.025

Neuron 53:829-841 (2007)

PubMed id: 17359918

Structure and mechanism of kainate receptor modulation by anions.

A.J.Plested, M.L.Mayer.

ABSTRACT

L-glutamate, the major excitatory neurotransmitter in the human brain, activates a family of ligand-gated ion channels, the major subtypes of which are named AMPA, kainate, and NMDA receptors. In common with many signal transduction proteins, glutamate receptors are modulated by ions and small molecules, including Ca(2+), Mg(2+), Zn(2+), protons, polyamines, and steroids. Strikingly, the activation of kainate receptors by glutamate requires the presence of both Na(+) and Cl(-) in the extracellular solution, and in the absence of these ions, receptor activity is abolished. Here, we identify the site and mechanism of action of anions. Surprisingly, we find that Cl(-) ions are essential structural components of kainate receptors. Cl(-) ions bind in a cavity formed at the interface between subunits in a dimer pair. In the absence of Cl(-), dimer stability is reduced, the rate of desensitization increases, and the fraction of receptors competent for activation by glutamate drops precipitously.

Selected figure(s)

Figure 4.
Figure 4. The Anion Binding Site Is Located in the Ligand Binding Core
(A) Cartoon of a kainate receptor subunit illustrating creation of the ATD(−) deletion construct and the block of desensitization when disulfide bond crosslinks are introduced in a ligand binding domain dimer assembly.
(B) Anion modulation of glutamate-evoked peak current amplitude, relative to the response in Cl^− (left) and desensitization rate (right), is similar in wild-type GluR6 and the ATD(−) construct. Data points show the mean ± SEM for at least five separate observations.
(C) Nondesensitizing kainate receptors formed by disulfide crosslinking the ligand binding domains of GluR6 are insensitive to modulation by anions. The bar plots show peak amplitude and percentage of desensitization for responses to glutamate recorded from the GluR6 Y490C L752C crosslinked mutant with fluoride, chloride, iodide, nitrate, or methanesulfonate as the extracellular anion. Data points show the mean ± SEM for at least five separate observations per condition.

Figure 5.
Figure 5. Molecular Structure of the Chloride Ion Binding Site
(A) Anomalous difference electron density map at 1.96 Å resolution for the GluR5 ligand binding core bromide complex contoured at 6 σ (purple). The Br^− ion sits on the molecular 2-fold between two subunits, colored red and blue respectively, for which helices J and D are labeled. Side chains that form salt bridges at the base and top of the anion binding site are drawn in stick configuration.
(B) Sigma A-weighted mF[o] − DF[c] electron density map at 2.11 Å resolution for the GluR5 ligand binding core sulfate complex contoured at 3 σ (blue); sulfate was omitted from the F[c] calculation. Note the altered conformation of Arg760 and the associated switch of salt bridges from intermolecular to intramolecular contacts.
(C) Stereo view of the GluR5 chloride complex rotated by 90° from the view in (A) with a sigma A-weighted mF[o] − DF[c] electron density map at 1.74 Å resolution contoured at 5 σ for the Cl^− ion (green), side chains (gray), and water molecules (blue); atoms drawn in stick configuration were omitted from the F[c] calculation.
(D) Molecular surface for domain 1 of the ligand binding core for one subunit in a GluR5 dimer assembly colored by surface curvature (concave green); the view is face-on to the anion binding site.
(E) Electrostatic surface potential map for the GluR5 anion binding site calculated with Cl^− removed from its binding site; the view is the same orientation as in (D).
(F) Amino acid sequence alignment and Cα movements (in Å) for the GluR5 and GluR2[flop] dimer crystal structures relative to the crystal structure of the R/G site unedited GluR2[flip]. AMPA receptor dimer structure.

The above figures are reprinted by permission from Cell Press: Neuron (2007, 53, 829-841) copyright 2007.

Figures were selected by an automated process.