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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 ligand electron densities and conformationsFo-Fc omit electron density maps for (a) ACPC bound to GluN1 LBD (chain A) and (b) t-ACBD bound to GluN2B LBD (chain D), contoured at 3 σ and 2.5 σ, respectively (Data set 1/Structure 1). c, d, e, Comparison of LBD in the full-length GluN1/GluN2B structure to isolated structures by aligning the D1 lobe. The angle of rotation relative to beta strand 10 is indicated for each. c, The ACPC-bound GluN1 LBD of the full-length structure (chain A, blue) is more open than the ACPC-bound isolated GluN1 LBD structure (PDB 1Y20, grey). d, The ACPC-bound GluN1 LBD of the full-length structure (chain A, blue) is more open than the glycine-bound isolated GluN1 LBD structure (PDB 2A5T, chain A, grey). e, The t-ACBD-bound GluN2B LBD of the full-length structure (chain D, orange) has a similar domain closure to the glutamate-bound isolated GluN2B LBD (PDB 2A5T, chain B, grey). f, GluN1/GluN2B LBD heterodimer (chains A and D) from the full-length receptor structure showing the separation of the D2 lobes, measured using the α-carbon atoms of residues Gly 664 and Gly 662, respectively. g, A similar measurement as in (f) using the equivalent residues in the context of the rat glycine/glutamate bound isolated GluN1/GluN2A LBDs (PDB 2A5T). h, The same measurement as in (g), except in the GluN1 antagonist/Glu2A glutamate-bound conformation (PDB 4NF4). Structures shown in panels c-f were derived from Data set 1/Structure 1 and are similar in conformation to the related domains derived from Data set 2/Structure 2 (see Extended Data Table 2).
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Figure 12: LBD ligand electron densities and conformationsFo-Fc omit electron density maps for (a) ACPC bound to GluN1 LBD (chain A) and (b) t-ACBD bound to GluN2B LBD (chain D), contoured at 3 σ and 2.5 σ, respectively (Data set 1/Structure 1). c, d, e, Comparison of LBD in the full-length GluN1/GluN2B structure to isolated structures by aligning the D1 lobe. The angle of rotation relative to beta strand 10 is indicated for each. c, The ACPC-bound GluN1 LBD of the full-length structure (chain A, blue) is more open than the ACPC-bound isolated GluN1 LBD structure (PDB 1Y20, grey). d, The ACPC-bound GluN1 LBD of the full-length structure (chain A, blue) is more open than the glycine-bound isolated GluN1 LBD structure (PDB 2A5T, chain A, grey). e, The t-ACBD-bound GluN2B LBD of the full-length structure (chain D, orange) has a similar domain closure to the glutamate-bound isolated GluN2B LBD (PDB 2A5T, chain B, grey). f, GluN1/GluN2B LBD heterodimer (chains A and D) from the full-length receptor structure showing the separation of the D2 lobes, measured using the α-carbon atoms of residues Gly 664 and Gly 662, respectively. g, A similar measurement as in (f) using the equivalent residues in the context of the rat glycine/glutamate bound isolated GluN1/GluN2A LBDs (PDB 2A5T). h, The same measurement as in (g), except in the GluN1 antagonist/Glu2A glutamate-bound conformation (PDB 4NF4). Structures shown in panels c-f were derived from Data set 1/Structure 1 and are similar in conformation to the related domains derived from Data set 2/Structure 2 (see Extended Data Table 2).

Mentions: The initial trigger for the eventual opening of the ion channel gate resides in agonist binding to the LBD clamshells. NMDA receptors require binding by agonists at both the GluN1 and GluN2 sites9, and here we have crystallized the receptor in complex with the partial agonists ACPC40 and t-ACBD41. Agonist binding results in closure of the LBD clamshell42 and separation of the region proximal to the M3 transmembrane helix18. Analysis of the GluN1 and GluN2B LBDs demonstrates that each of the two GluN1 and GluN2B clamshells adopt similar conformations (Extended Data Table 3). Moreover, the degree of closure is similar to that observed for the isolated LBDs (Extended Data Fig. 6), except that they are both slightly more open in comparison to the isolated domains, perhaps due to direct linkage to the ion channel. Separation of the region proximal to the M3 helices is similar between the equivalent residues in the LBD dimers of the full length receptor and in the glycine/glutamate complex of the isolated GluN1/GluN2A LBDs yet longer than in an LBD antagonist (DCKA)/glutamate complex (Extended Data Fig. 6f-h). Thus by this metric the LBD dimers adopt an agonist-bound, activated conformation.


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 ligand electron densities and conformationsFo-Fc omit electron density maps for (a) ACPC bound to GluN1 LBD (chain A) and (b) t-ACBD bound to GluN2B LBD (chain D), contoured at 3 σ and 2.5 σ, respectively (Data set 1/Structure 1). c, d, e, Comparison of LBD in the full-length GluN1/GluN2B structure to isolated structures by aligning the D1 lobe. The angle of rotation relative to beta strand 10 is indicated for each. c, The ACPC-bound GluN1 LBD of the full-length structure (chain A, blue) is more open than the ACPC-bound isolated GluN1 LBD structure (PDB 1Y20, grey). d, The ACPC-bound GluN1 LBD of the full-length structure (chain A, blue) is more open than the glycine-bound isolated GluN1 LBD structure (PDB 2A5T, chain A, grey). e, The t-ACBD-bound GluN2B LBD of the full-length structure (chain D, orange) has a similar domain closure to the glutamate-bound isolated GluN2B LBD (PDB 2A5T, chain B, grey). f, GluN1/GluN2B LBD heterodimer (chains A and D) from the full-length receptor structure showing the separation of the D2 lobes, measured using the α-carbon atoms of residues Gly 664 and Gly 662, respectively. g, A similar measurement as in (f) using the equivalent residues in the context of the rat glycine/glutamate bound isolated GluN1/GluN2A LBDs (PDB 2A5T). h, The same measurement as in (g), except in the GluN1 antagonist/Glu2A glutamate-bound conformation (PDB 4NF4). Structures shown in panels c-f were derived from Data set 1/Structure 1 and are similar in conformation to the related domains derived from Data set 2/Structure 2 (see Extended Data Table 2).
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Figure 12: LBD ligand electron densities and conformationsFo-Fc omit electron density maps for (a) ACPC bound to GluN1 LBD (chain A) and (b) t-ACBD bound to GluN2B LBD (chain D), contoured at 3 σ and 2.5 σ, respectively (Data set 1/Structure 1). c, d, e, Comparison of LBD in the full-length GluN1/GluN2B structure to isolated structures by aligning the D1 lobe. The angle of rotation relative to beta strand 10 is indicated for each. c, The ACPC-bound GluN1 LBD of the full-length structure (chain A, blue) is more open than the ACPC-bound isolated GluN1 LBD structure (PDB 1Y20, grey). d, The ACPC-bound GluN1 LBD of the full-length structure (chain A, blue) is more open than the glycine-bound isolated GluN1 LBD structure (PDB 2A5T, chain A, grey). e, The t-ACBD-bound GluN2B LBD of the full-length structure (chain D, orange) has a similar domain closure to the glutamate-bound isolated GluN2B LBD (PDB 2A5T, chain B, grey). f, GluN1/GluN2B LBD heterodimer (chains A and D) from the full-length receptor structure showing the separation of the D2 lobes, measured using the α-carbon atoms of residues Gly 664 and Gly 662, respectively. g, A similar measurement as in (f) using the equivalent residues in the context of the rat glycine/glutamate bound isolated GluN1/GluN2A LBDs (PDB 2A5T). h, The same measurement as in (g), except in the GluN1 antagonist/Glu2A glutamate-bound conformation (PDB 4NF4). Structures shown in panels c-f were derived from Data set 1/Structure 1 and are similar in conformation to the related domains derived from Data set 2/Structure 2 (see Extended Data Table 2).
Mentions: The initial trigger for the eventual opening of the ion channel gate resides in agonist binding to the LBD clamshells. NMDA receptors require binding by agonists at both the GluN1 and GluN2 sites9, and here we have crystallized the receptor in complex with the partial agonists ACPC40 and t-ACBD41. Agonist binding results in closure of the LBD clamshell42 and separation of the region proximal to the M3 transmembrane helix18. Analysis of the GluN1 and GluN2B LBDs demonstrates that each of the two GluN1 and GluN2B clamshells adopt similar conformations (Extended Data Table 3). Moreover, the degree of closure is similar to that observed for the isolated LBDs (Extended Data Fig. 6), except that they are both slightly more open in comparison to the isolated domains, perhaps due to direct linkage to the ion channel. Separation of the region proximal to the M3 helices is similar between the equivalent residues in the LBD dimers of the full length receptor and in the glycine/glutamate complex of the isolated GluN1/GluN2A LBDs yet longer than in an LBD antagonist (DCKA)/glutamate complex (Extended Data Fig. 6f-h). Thus by this metric the LBD dimers adopt an agonist-bound, activated conformation.

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
Related in: MedlinePlus