PDBsum entry 3c35

Membrane protein

PDB id: 3c35

Contents

Protein chains

254 a.a.

Ligands

KAI ×2

GOL ×3

Metals

_CS ×13

_CL

Waters ×400

References listed in PDB file

Key reference

Title

Molecular basis of kainate receptor modulation by sodium.

Authors

A.J.Plested, R.Vijayan, P.C.Biggin, M.L.Mayer.

Ref.

Neuron, 2008, 58, 720-735.

PubMed id

18549784

Abstract

Membrane proteins function in a polarized ionic environment with sodium-rich extracellular and potassium-rich intracellular solutions. Glutamate receptors that mediate excitatory synaptic transmission in the brain show unusual sensitivity to external ions, resulting in an apparent requirement for sodium in order for glutamate to activate kainate receptors. Here, we solve the structure of the Na(+)-binding sites and determine the mechanism by which allosteric anions and cations regulate ligand-binding dimer stability, and hence the rate of desensitization and receptor availability for gating by glutamate. We establish a stoichiometry for binding of 2 Na(+) to 1 Cl(-) and show that allosteric anions and cations bind at physically discrete sites with strong electric fields, that the binding sites are not saturated in CSF, and that the requirement of kainate receptors for Na(+) occurs simply because other cations bind with lower affinity and have lower efficacy compared to Na(+).

Secondary reference #1

Title

Structure and mechanism of kainate receptor modulation by anions.

Authors

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

Ref.

Neuron, 2007, 53, 829-841. [DOI no: 10.1016/j.neuron.2007.02.025]

PubMed id

17359918

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 reproduced from the cited reference with permission from Cell Press

Secondary reference #2

Title

Crystal structures of the glur5 and glur6 ligand binding cores: molecular mechanisms underlying kainate receptor selectivity.

Author

M.L.Mayer.

Ref.

Neuron, 2005, 45, 539-552. [DOI no: 10.1016/j.neuron.2005.01.031]

PubMed id

15721240

Figure 4.
Figure 4. Docking GluR5-Selective Ligands in the GluR6 and GluR5 Ligand Binding Sites

Figure 7.
Figure 7. Interdomain Contacts in GluR5 and GluR2

The above figures are reproduced from the cited reference with permission from Cell Press