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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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LBD layer forms a ring-like structurea, The GluN1/GluN2B LBD and TMD, showing that the pseudo 2-fold axes of the B/C and A/D LBD heterodimers diverge with an angle of 60°. The boxed areas define regions of LBD dimer-dimer contacts shown in panels (g) and (h). b, View of the antagonist-bound state of the GluA2 AMPA receptor, which shows that the 2-fold axes of the LBD dimers diverge by an angle of 40.9°c, View from the extracellular side of the membrane, along the overall 2-fold axis of the receptor, showing the LBDs of the GluN1 and GluN2B subunits, with the LBD heterodimer interface of the B/C subunits emphasized by a box. d, GluA2 LBD layer, illustrating how the interface between the B/C and A/D subunits has increased in comparison to the NMDA receptor LBD layer. e, Schematic of the LBD layer, showing the NMDA receptor B/C and A/D heterodimers as rectangles (solid lines) and illustrating the translational shift of the A/D subunits in the AMPA receptor (dotted lines). The asterisk indicates the dimer-dimer interface. f,g,h, Closeup view of the canonical D1-D1 intradimer interface32, together with views of the interactions at the interdimer interfaces in panels (g) and (h). The domains from Structure 2 are shown, with GluN1 subunits in blue and GluN2B subunits in orange.
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Figure 3: LBD layer forms a ring-like structurea, The GluN1/GluN2B LBD and TMD, showing that the pseudo 2-fold axes of the B/C and A/D LBD heterodimers diverge with an angle of 60°. The boxed areas define regions of LBD dimer-dimer contacts shown in panels (g) and (h). b, View of the antagonist-bound state of the GluA2 AMPA receptor, which shows that the 2-fold axes of the LBD dimers diverge by an angle of 40.9°c, View from the extracellular side of the membrane, along the overall 2-fold axis of the receptor, showing the LBDs of the GluN1 and GluN2B subunits, with the LBD heterodimer interface of the B/C subunits emphasized by a box. d, GluA2 LBD layer, illustrating how the interface between the B/C and A/D subunits has increased in comparison to the NMDA receptor LBD layer. e, Schematic of the LBD layer, showing the NMDA receptor B/C and A/D heterodimers as rectangles (solid lines) and illustrating the translational shift of the A/D subunits in the AMPA receptor (dotted lines). The asterisk indicates the dimer-dimer interface. f,g,h, Closeup view of the canonical D1-D1 intradimer interface32, together with views of the interactions at the interdimer interfaces in panels (g) and (h). The domains from Structure 2 are shown, with GluN1 subunits in blue and GluN2B subunits in orange.

Mentions: The agonist-binding LBDs of the NMDA receptor are organized as a nearly equivalent pair of GluN1/GluN2B heterodimers where each GluN1/GluN2B heterodimer (Figs. 3a, 3c) closely resembles the water-soluble heterodimers of the isolated GluN1/GluN2A LBDs32 and the homodimeric assemblies of AMPA18 and kainate receptor37 LBDs in non desensitized conformations. Moreover, the arrangement is similar to that previously observed in the structure of the full length AMPA receptor (Figs. 3b, 3d)28, although here the electron density for the GluN1 and GluN2B LBDs in chains B and C is weak, perhaps due to an absence of lattice contacts. In comparing this NMDA receptor structure to the antagonist-bound state of the AMPA receptor, the extent to which the local 2-fold axes of each LBD dimer are tipped off of the overall molecular 2-fold axis of symmetry differ (Figs. 3a, b). In addition, inspection of the GluN1/GluN2B and AMPA receptor LBD layers, viewed from the ‘top’ (Figs. 3c, d), shows that there is a relative translation, or shift, of the LBD dimers along the interdimer interface (Fig. 3e). Using helix J to align the B/C LBDs, the A/D LBD dimer in the AMPA receptor has undergone a translational ‘shift’ of ~15 Å relative to the A/D NMDA receptor LBD heterodimer. While we do not know if these differences in LBD dimer ‘roll’ angle (Figs. 3a, 3b) and translational ‘shift’ (Fig. 3e) are due to inherent differences between NMDA and AMPA receptors or to the closed-blocked state of the NMDA receptor versus the competitive antagonist-bound form of the AMPA receptor, or to both factors, this analysis illustrates conformational mobility of the LBD dimers perhaps related to how the LBD couples agonist-binding to the TMD.


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)

LBD layer forms a ring-like structurea, The GluN1/GluN2B LBD and TMD, showing that the pseudo 2-fold axes of the B/C and A/D LBD heterodimers diverge with an angle of 60°. The boxed areas define regions of LBD dimer-dimer contacts shown in panels (g) and (h). b, View of the antagonist-bound state of the GluA2 AMPA receptor, which shows that the 2-fold axes of the LBD dimers diverge by an angle of 40.9°c, View from the extracellular side of the membrane, along the overall 2-fold axis of the receptor, showing the LBDs of the GluN1 and GluN2B subunits, with the LBD heterodimer interface of the B/C subunits emphasized by a box. d, GluA2 LBD layer, illustrating how the interface between the B/C and A/D subunits has increased in comparison to the NMDA receptor LBD layer. e, Schematic of the LBD layer, showing the NMDA receptor B/C and A/D heterodimers as rectangles (solid lines) and illustrating the translational shift of the A/D subunits in the AMPA receptor (dotted lines). The asterisk indicates the dimer-dimer interface. f,g,h, Closeup view of the canonical D1-D1 intradimer interface32, together with views of the interactions at the interdimer interfaces in panels (g) and (h). The domains from Structure 2 are shown, with GluN1 subunits in blue and GluN2B subunits in orange.
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Related In: Results  -  Collection

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Figure 3: LBD layer forms a ring-like structurea, The GluN1/GluN2B LBD and TMD, showing that the pseudo 2-fold axes of the B/C and A/D LBD heterodimers diverge with an angle of 60°. The boxed areas define regions of LBD dimer-dimer contacts shown in panels (g) and (h). b, View of the antagonist-bound state of the GluA2 AMPA receptor, which shows that the 2-fold axes of the LBD dimers diverge by an angle of 40.9°c, View from the extracellular side of the membrane, along the overall 2-fold axis of the receptor, showing the LBDs of the GluN1 and GluN2B subunits, with the LBD heterodimer interface of the B/C subunits emphasized by a box. d, GluA2 LBD layer, illustrating how the interface between the B/C and A/D subunits has increased in comparison to the NMDA receptor LBD layer. e, Schematic of the LBD layer, showing the NMDA receptor B/C and A/D heterodimers as rectangles (solid lines) and illustrating the translational shift of the A/D subunits in the AMPA receptor (dotted lines). The asterisk indicates the dimer-dimer interface. f,g,h, Closeup view of the canonical D1-D1 intradimer interface32, together with views of the interactions at the interdimer interfaces in panels (g) and (h). The domains from Structure 2 are shown, with GluN1 subunits in blue and GluN2B subunits in orange.
Mentions: The agonist-binding LBDs of the NMDA receptor are organized as a nearly equivalent pair of GluN1/GluN2B heterodimers where each GluN1/GluN2B heterodimer (Figs. 3a, 3c) closely resembles the water-soluble heterodimers of the isolated GluN1/GluN2A LBDs32 and the homodimeric assemblies of AMPA18 and kainate receptor37 LBDs in non desensitized conformations. Moreover, the arrangement is similar to that previously observed in the structure of the full length AMPA receptor (Figs. 3b, 3d)28, although here the electron density for the GluN1 and GluN2B LBDs in chains B and C is weak, perhaps due to an absence of lattice contacts. In comparing this NMDA receptor structure to the antagonist-bound state of the AMPA receptor, the extent to which the local 2-fold axes of each LBD dimer are tipped off of the overall molecular 2-fold axis of symmetry differ (Figs. 3a, b). In addition, inspection of the GluN1/GluN2B and AMPA receptor LBD layers, viewed from the ‘top’ (Figs. 3c, d), shows that there is a relative translation, or shift, of the LBD dimers along the interdimer interface (Fig. 3e). Using helix J to align the B/C LBDs, the A/D LBD dimer in the AMPA receptor has undergone a translational ‘shift’ of ~15 Å relative to the A/D NMDA receptor LBD heterodimer. While we do not know if these differences in LBD dimer ‘roll’ angle (Figs. 3a, 3b) and translational ‘shift’ (Fig. 3e) are due to inherent differences between NMDA and AMPA receptors or to the closed-blocked state of the NMDA receptor versus the competitive antagonist-bound form of the AMPA receptor, or to both factors, this analysis illustrates conformational mobility of the LBD dimers perhaps related to how the LBD couples agonist-binding to the TMD.

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