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NMDA receptor structures reveal subunit arrangement and pore architecture.

Lee CH, Lü W, Michel JC, Goehring A, Du J, Song X, Gouaux E - Nature (2014)

Bottom Line: Receptor subunits are arranged in a 1-2-1-2 fashion, demonstrating extensive interactions between the amino-terminal and ligand-binding domains.The transmembrane domains harbour a closed-blocked ion channel, a pyramidal central vestibule lined by residues implicated in binding ion channel blockers and magnesium, and a ∼twofold symmetric arrangement of ion channel pore loops.These structures provide new insights into the architecture, allosteric coupling and ion channel function of NMDA receptors.

View Article: PubMed Central - PubMed

Affiliation: 1] Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA [2].

ABSTRACT
N-methyl-d-aspartate (NMDA) receptors are Hebbian-like coincidence detectors, requiring binding of glycine and glutamate in combination with the relief of voltage-dependent magnesium block to open an ion conductive pore across the membrane bilayer. Despite the importance of the NMDA receptor in the development and function of the brain, a molecular structure of an intact receptor has remained elusive. Here we present X-ray crystal structures of the Xenopus laevis GluN1-GluN2B NMDA receptor with the allosteric inhibitor, Ro25-6981, partial agonists and the ion channel blocker, MK-801. Receptor subunits are arranged in a 1-2-1-2 fashion, demonstrating extensive interactions between the amino-terminal and ligand-binding domains. The transmembrane domains harbour a closed-blocked ion channel, a pyramidal central vestibule lined by residues implicated in binding ion channel blockers and magnesium, and a ∼twofold symmetric arrangement of ion channel pore loops. These structures provide new insights into the architecture, allosteric coupling and ion channel function of NMDA receptors.

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Schematic of the NMDA receptora, Shown is a single ATD heterodimer, two LBD ‘clamshells’ residing in different LBD heterodimers, and the TMD of GluN2B subunits, emphasizing only the M2, pore loop and M3 elements. The line connecting the M3 helix on the right is ‘broken’ to illustrate that it is connected to the GluN2B LBD ‘behind’ the shown GluN1 LBD. Double-headed arrows suggest possible movements of ATDs within an ATD heterodimer. b, Rotation of the receptor schematic shown in panel (a) by ~120° showing two ATD heterodimers, a single LBD heterodimer and the TMD of GluN1 subunits. Double-headed arrows show conformational movements between ATD heterodimers observed in the structures described here. The α5 helices, harboring the K216C crosslink, are shown as rectangles at the R2-R2 interface. In both schematics, we emphasize how the R2 lobes of the ATDs are positioned such they could modulate inter- and intradimer LBD interfaces and, in turn, the ion channel gate.
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Figure 6: Schematic of the NMDA receptora, Shown is a single ATD heterodimer, two LBD ‘clamshells’ residing in different LBD heterodimers, and the TMD of GluN2B subunits, emphasizing only the M2, pore loop and M3 elements. The line connecting the M3 helix on the right is ‘broken’ to illustrate that it is connected to the GluN2B LBD ‘behind’ the shown GluN1 LBD. Double-headed arrows suggest possible movements of ATDs within an ATD heterodimer. b, Rotation of the receptor schematic shown in panel (a) by ~120° showing two ATD heterodimers, a single LBD heterodimer and the TMD of GluN1 subunits. Double-headed arrows show conformational movements between ATD heterodimers observed in the structures described here. The α5 helices, harboring the K216C crosslink, are shown as rectangles at the R2-R2 interface. In both schematics, we emphasize how the R2 lobes of the ATDs are positioned such they could modulate inter- and intradimer LBD interfaces and, in turn, the ion channel gate.

Mentions: The GluN1/GluN2B structure harbors an overall 2-fold symmetry, a layered dimer-of-dimers arrangement of subunits and a positioning of NR1 and NR2B subunits in the A/C and B/D positions defined by the full length GluA2 receptor28 (Supplementary Video 1). The rich interdigitations and covalent linkage of the R2 lobes of the ATDs to the LBDs provides molecular routes for transmission of allosteric signals to the glycine and glutamate-binding LBD layer, which is organized as a ring of heterodimeric units above the transmembrane ion channel (Fig. 6). Despite closure of the LBD ‘clamshells’ around partial agonists and an intact ‘non desensitized’ D1-D1 interface of the LBD heterodimers, the ion channel gate is in a closed-blocked state, providing the first insights into the structural basis for allosteric inactivation of a NMDA receptor and suggesting that plasticity of the LBD layer may provide a mechanism for modulation of receptor gating. Departing from the 4-fold symmetry of the GluA2 transmembrane domain, the pore loops of the NMDA receptor are approximately 2-fold symmetric. The allosteric antagonist-bound GluN1/GluN2B structure provides a molecular blueprint for the development of new therapeutic agents and a structural framework for biophysical mechanisms of allosteric modulation, gating and ion channel function, as well as a spring board for future studies directed toward determining structures of resting, open and desensitized states and defining locations of ion binding sites.


NMDA receptor structures reveal subunit arrangement and pore architecture.

Lee CH, Lü W, Michel JC, Goehring A, Du J, Song X, Gouaux E - Nature (2014)

Schematic of the NMDA receptora, Shown is a single ATD heterodimer, two LBD ‘clamshells’ residing in different LBD heterodimers, and the TMD of GluN2B subunits, emphasizing only the M2, pore loop and M3 elements. The line connecting the M3 helix on the right is ‘broken’ to illustrate that it is connected to the GluN2B LBD ‘behind’ the shown GluN1 LBD. Double-headed arrows suggest possible movements of ATDs within an ATD heterodimer. b, Rotation of the receptor schematic shown in panel (a) by ~120° showing two ATD heterodimers, a single LBD heterodimer and the TMD of GluN1 subunits. Double-headed arrows show conformational movements between ATD heterodimers observed in the structures described here. The α5 helices, harboring the K216C crosslink, are shown as rectangles at the R2-R2 interface. In both schematics, we emphasize how the R2 lobes of the ATDs are positioned such they could modulate inter- and intradimer LBD interfaces and, in turn, the ion channel gate.
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Related In: Results  -  Collection

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Figure 6: Schematic of the NMDA receptora, Shown is a single ATD heterodimer, two LBD ‘clamshells’ residing in different LBD heterodimers, and the TMD of GluN2B subunits, emphasizing only the M2, pore loop and M3 elements. The line connecting the M3 helix on the right is ‘broken’ to illustrate that it is connected to the GluN2B LBD ‘behind’ the shown GluN1 LBD. Double-headed arrows suggest possible movements of ATDs within an ATD heterodimer. b, Rotation of the receptor schematic shown in panel (a) by ~120° showing two ATD heterodimers, a single LBD heterodimer and the TMD of GluN1 subunits. Double-headed arrows show conformational movements between ATD heterodimers observed in the structures described here. The α5 helices, harboring the K216C crosslink, are shown as rectangles at the R2-R2 interface. In both schematics, we emphasize how the R2 lobes of the ATDs are positioned such they could modulate inter- and intradimer LBD interfaces and, in turn, the ion channel gate.
Mentions: The GluN1/GluN2B structure harbors an overall 2-fold symmetry, a layered dimer-of-dimers arrangement of subunits and a positioning of NR1 and NR2B subunits in the A/C and B/D positions defined by the full length GluA2 receptor28 (Supplementary Video 1). The rich interdigitations and covalent linkage of the R2 lobes of the ATDs to the LBDs provides molecular routes for transmission of allosteric signals to the glycine and glutamate-binding LBD layer, which is organized as a ring of heterodimeric units above the transmembrane ion channel (Fig. 6). Despite closure of the LBD ‘clamshells’ around partial agonists and an intact ‘non desensitized’ D1-D1 interface of the LBD heterodimers, the ion channel gate is in a closed-blocked state, providing the first insights into the structural basis for allosteric inactivation of a NMDA receptor and suggesting that plasticity of the LBD layer may provide a mechanism for modulation of receptor gating. Departing from the 4-fold symmetry of the GluA2 transmembrane domain, the pore loops of the NMDA receptor are approximately 2-fold symmetric. The allosteric antagonist-bound GluN1/GluN2B structure provides a molecular blueprint for the development of new therapeutic agents and a structural framework for biophysical mechanisms of allosteric modulation, gating and ion channel function, as well as a spring board for future studies directed toward determining structures of resting, open and desensitized states and defining locations of ion binding sites.

Bottom Line: Receptor subunits are arranged in a 1-2-1-2 fashion, demonstrating extensive interactions between the amino-terminal and ligand-binding domains.The transmembrane domains harbour a closed-blocked ion channel, a pyramidal central vestibule lined by residues implicated in binding ion channel blockers and magnesium, and a ∼twofold symmetric arrangement of ion channel pore loops.These structures provide new insights into the architecture, allosteric coupling and ion channel function of NMDA receptors.

View Article: PubMed Central - PubMed

Affiliation: 1] Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA [2].

ABSTRACT
N-methyl-d-aspartate (NMDA) receptors are Hebbian-like coincidence detectors, requiring binding of glycine and glutamate in combination with the relief of voltage-dependent magnesium block to open an ion conductive pore across the membrane bilayer. Despite the importance of the NMDA receptor in the development and function of the brain, a molecular structure of an intact receptor has remained elusive. Here we present X-ray crystal structures of the Xenopus laevis GluN1-GluN2B NMDA receptor with the allosteric inhibitor, Ro25-6981, partial agonists and the ion channel blocker, MK-801. Receptor subunits are arranged in a 1-2-1-2 fashion, demonstrating extensive interactions between the amino-terminal and ligand-binding domains. The transmembrane domains harbour a closed-blocked ion channel, a pyramidal central vestibule lined by residues implicated in binding ion channel blockers and magnesium, and a ∼twofold symmetric arrangement of ion channel pore loops. These structures provide new insights into the architecture, allosteric coupling and ion channel function of NMDA receptors.

Show MeSH