Structural basis of kainate subtype glutamate receptor desensitization

Abstract

Glutamate receptors are ligand gated tetrameric ion channels that mediate synaptic transmission in the central nervous system. They are instrumental in vertebrate cognition and their dysfunction underlies diverse diseases1,2. In both the resting and desensitized states of AMPA and kainate subtype glutamate receptors the ion channels are closed while the ligand binding domain, which is physically coupled to the channel, adopts dramatically different conformations3–6. Without an atomic model for the desensitized state, it is not possible to address a central question in receptor gating: how the resting and desensitized receptor states both display closed ion channels, even though they have major differences in quaternary structure of the ligand binding domain. By determining the cryo-EM structure of the kainate receptor GluK2 subtype in its desensitized state at 3.8 Å resolution, we show that desensitization is characterized by establishment of a ring-like structure in the ligand binding domain layer of the receptor. Formation of this “desensitization ring” is mediated by staggered helix contacts between adjacent subunits, which leads to a pseudo four-fold symmetric arrangement of the ligand binding domains, illustrating subtle changes in symmetry that are at the heart of the gating mechanism. Disruption of the desensitization ring is likely the key switch that enables restoration of the receptor to its resting state, thereby completing the gating cycle.

Structural Bases of Desensitization in AMPA Receptor-Auxiliary Subunit Complexes

“…Given the apparent strengthening of desensitization in AMPARs carrying G725C and S729C substitutions (Armstrong et al, 2006; Plested and Mayer, 2009; Yelshanskaya et al, 2014) and weakening of desensitization by positive allosteric modulators and mutations at the D1-D1 interface (Gonzalez et al, 2010; Jin et al, 2005; Nayeem et al, 2009; Priel et al, 2006; Stern-Bach et al, 1998; Sun et al, 2002; Weston et al, 2006), such similarities supports the idea that the GluA2-2xGSG1L Quis structure represents a desensitized state. The latter conclusion is also consistent with transformation of the LBD layer assembly in GluA2-2xGSG1L ZK towards its more 4-fold symmetrical arrangement in GluA2-2xGSG1L Quis (Figure 6E–F,L), similar to the desensitized structure of GluK2 (Meyerson et al, 2016; Meyerson et al, 2014). …”

“…In contrast, the A/C LBDs in GluK2 bound to the full agonist (2S,4R)-4-methylglutamate are at similar positions as in the GluA2 NOW structure but the B/D LBDs rotate clockwise by 125° around their own axes (Figure 7C,F), presenting completely different surfaces at the intersubunit interfaces. As a result, helices E and G in the B/D LBDs, which do not contribute to intersubunit interfaces in the GluA2 structures, combine with helices E and G in subunits A and C of GluK2 to assemble a pseudo fourfold symmetric “desensitization ring” in the center of the LBD layer (Meyerson et al, 2016) (Figure 7F). Such a dramatic rearrangement of LBDs in GluK2 allows the M3 transmembrane segments in subunits B and D to adopt similar secondary structures as in subunits A and C (Figure 7I).…”

Activation and Desensitization Mechanism of AMPA Receptor-TARP Complex by Cryo-EM

“…Cysteine mutagenesis and electrophysiological studies carried out on the intact and ΔATD receptors, along with crystallographic studies on the isolated LBD ‘dimers’, suggested that rupture of the LBD dimer D1-D1 interface was sufficient to promote receptor desensitization (Armstrong et al, 2006). By contrast, cryo-EM studies of isolated AMPA receptors and the closely related kainate receptors suggest that there are, instead, large scale rearrangements of the LBD layer from 2-fold to ~4-fold symmetry (Meyerson et al, 2016; Meyerson et al, 2014). A low resolution x-ray study of an intact AMPA receptor, as well as cryo-EM studies, are also suggestive of large scale LBD rearrangements upon receptor desensitization (Dürr et al, 2014).…”

Cryo-EM structures of the triheteromeric NMDA receptor and its allosteric modulation

“…In non-NMDARs, direct interactions between the ATD and LBD layers are minimal. Therefore, even if the ATDs undergo ligand-induced movements, there are few molecular routes for transduction of conformational changes and thus the ATDs of non-NMDARs do not markedly modulate ion channel gating (36, 41–43, 52). By contrast, there are multiple distinct contacts between the ATD and LBD layers in NMDARs, and thus a number of mechanisms by which movements of the ATDs can be transduced to the LBD layer and, subsequently, to the TMD to modulate ion channel activity (38, 53, 54).…”