Abstract
Glutamate transmission and activation of ionotropic glutamate receptors are the fundamental means by which neurons control their excitability and neuroplasticity1. The N-methyl-d-aspartate receptor (NMDAR) is unique among all ligand-gated channels, requiring two ligands—glutamate and glycine—for activation. These receptors function as heterotetrameric ion channels, with the channel opening dependent on the simultaneous binding of glycine and glutamate to the extracellular ligand-binding domains (LBDs) of the GluN1 and GluN2 subunits, respectively2,3. The exact molecular mechanism for channel gating by the two ligands has been unclear, particularly without structures representing the open channel and apo states. Here we show that the channel gate opening requires tension in the linker connecting the LBD and transmembrane domain (TMD) and rotation of the extracellular domain relative to the TMD. Using electron cryomicroscopy, we captured the structure of the GluN1–GluN2B (GluN1–2B) NMDAR in its open state bound to a positive allosteric modulator. This process rotates and bends the pore-forming helices in GluN1 and GluN2B, altering the symmetry of the TMD channel from pseudofourfold to twofold. Structures of GluN1–2B NMDAR in apo and single-liganded states showed that binding of either glycine or glutamate alone leads to distinct GluN1–2B dimer arrangements but insufficient tension in the LBD–TMD linker for channel opening. This mechanistic framework identifies a key determinant for channel gating and a potential pharmacological strategy for modulating NMDAR activity.
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Data availability
Cryo-EM density maps have been deposited in the Electron Microscopy Data Bank (EMDB) under accession codes, EMD-43779 (GluN1–2B, EU-1622-240-bound, open conformation, C2 symmetry), EMD-44586 (GluN1–2B, EU-1622-240-bound, open conformation, C1 symmetry), EMD-43780 (GluN1–2B, non-active1 conformation), EMD-43781 (GluN1–2B, apo/apo conformation), EMD-43782 (GluN1–2B, glycine/apo), EMD-43783 (GluN1–2B, apo/glutamate). The structural coordinates have been deposited in the RCSB Protein Data Bank (PDB) under accession codes, 9ARE (GluN1–2B, EU-1622-240-bound, open conformation, C2 symmetry), 9BIB (GluN1–2B, EU-1622-240-bound, open conformation, C1 symmetry), 9ARF (GluN1–2B, non-active1 conformation), 9ARG (GluN1–2B, apo/apo conformation), 9ARH (GluN1–2B, glycine/apo), 9ARI (GluN1–2B, apo/glutamate). The structure of pre-active GluN1–2B NMDAR is available in the PDB under the accession code 6WI1. The structural coordinates of pre-active, open and desensitized GluA2 AMPAR are available in the PDB under the accession codes 4U5C, 5WEO and 7RZA, respectively. Source data are provided with this paper.
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Acknowledgements
We thank N. Simorowski for technical support; D. Thomas and M. Wang for managing the cryo-EM facility and computing facility, respectively, at Cold Spring Harbor Laboratory (CSHL); and A. Sobolevsky and L. Anson for critical comments on this work. This work was supported by the National Institutes of Health (NIH) (NS111745 and MH085926 to H.F. and NS111619 to S.F.T.), Austin’s purpose (to H.F. and S.F.T.), Robertson funds at CSHL, Doug Fox Alzheimer’s fund, Heartfelt Wing Alzheimer’s fund and the Gertrude and Louis Feil Family Trust (to H.F.). We performed the computational work with assistance from an NIH grant (S10OD028632-01).
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T.-H.C. and H.F. conceived the project. T.-H.C. obtained all cryo-EM structures and conducted electrophysiology experiments in Fig. 3e,f. M.E. conducted molecular dynamics simulations. R.G.F., N.S.A., S.P. and D.C.L. synthesized the PAM compound. E.Z.U. and S.F.T. conducted electrophysiology experiments in Fig. 1a and 3c,d. T.-H.C., M.E. and H.F. wrote the manuscript with input from all authors.
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S.F.T. is a member of the medical advisory boards for the CureGRIN Foundation and the GRIN2B Foundation; a member of the scientific advisory boards for Sage Therapeutics, Eumentis Therapeutics, and Neurocrine; a Senior Advisor for GRIN Therapeutics; a co-founder of NeurOp, Inc and AgriThera, Inc.; and is on the Board of Directors for NeurOp Inc. D.C.L. is on the Board of Directors for NeurOp Inc. Several authors (R.G.F., N.S.A., S.P., S.F.T., D.C.L.) are co-inventors on Emory-owned IP involving NMDA receptor modulators. The other authors declare no competing interests.
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Extended data figures and tables
Extended Data Fig. 1 Single-particle cryo-EM on glycine-, glutamate-, and EU-1622-240-bound rat GluN1–2B NMDAR.
a, A representative EM micrograph, 2D classes, and the 3D classification and refinement workflow. The scale bar on the micrograph equates to 49.5 nm. b, d, and g, Orientation distribution maps of the particles used in reconstructing the final map of the non-active1 (b), open C1 (d), and open C2 (g) structures. c, e, and f, Local resolution estimation calculated by ResMap for the non-active1 (c), open C1 (e), and open C2 (f) structures. h and k, Post-processing analysis of open (h) and non-active1 (k) state structures. The masked (blue) and unmasked (red) Fourier shell correlation (FSC) curves of two half maps (top), map vs. model (bottom). i and l, Representative zoom-in views of the cryo-EM density in conserved regions for both open (i) and non-active1 (l) states fitted with molecular models. A red arrowhead indicates the starting residue of the GluN2B M3′ helix bending in the open state structure. j, A zoom-in view of the cryo-EM density of the bound EU-1622-240 compound in the open state structure (red arrow).
Extended Data Fig. 2 Structural comparison of open state, pre-active, and non-active1 states.
a, Cartoon representation of GluN1–2B NMDARs in the open state. Dotted lines on the left panel enclose one GluN1-2B ATD dimer and two GluN1-2B LBD dimers, whereas the ones on the right panel enclose the GluN1-2B LBD heterodimer. The color codes are as in Fig. 1. b-c, Comparison of the LBD dimer arrangements and the interfaces involving GluN2B ATD, GluN2B L1′, and GluN1 L2 (arrows) between the open and pre-active (gray) states (b) and the open and non-active1 (gray) states (c). The arrangements are similar between the open and pre-active states but show divergence between the open and non-active states, especially the positionings of the L1′ and L2 due to the dimer rotation (double-line arrows). d-e, Comparison of the GluN1-2B ATD dimers and GluN2B ATD bi-lobe structures between the open and pre-active (gray) states (d) and between the open and non-active1 states (e). Open and pre-active states exhibit similar conformations, whereas substantial changes are evident between the open and non-active1 states, as highlighted by the differences in the α4′-α5 distances (panel e, left). GluN2B ATD bi-lobe structure is ~13° more open in the open state than the non-active1 state (e, right).
Extended Data Fig. 3 PMF calculations.
a, All-atom Potential of Mean Force (PMF) calculations for the TMD channel highlight a more favorable free energy for Na+ ions around the VIVI gate and SYTANLAAF motif in the open state (blue), as opposed to the pre-active (green) and non-active1 (red) states, consistent with the gate opening and pore dilation in the open state structure. The placement of Cl- is shown to be unfavorable, indicated by the positive free energy level (purple), consistent with the cation selectivity of the NMDAR channel. b, Block analysis of the PMF calculation. Each color represents an additional block where the PMF was rerun with two ns of additional data. The two final PMF blocks for all systems were within thermal energy, demonstrating convergence.
Extended Data Fig. 4 Single-particle analysis on rat GluN1-2B NMDAR in apo/apo state.
a, A representative EM micrograph, 2D classes, and the 3D classification and refinement workflow. The scale bar on the micrograph equates to 49.5 nm. b, An orientation distribution map of the particles used to reconstruct the final map. c, Local resolution estimation calculated by ResMap. d, Post-processing analysis. The masked (blue) and unmasked (red) Fourier shell correlation (FSC) curves of two half maps (top), map vs. model (bottom). e, Representative zoom-in views of the cryo-EM density in different conserved regions fitted with molecular models.
Extended Data Fig. 5 Single-particle analysis on rat GluN1-2B NMDAR in gly/apo state.
a, A representative EM micrograph, 2D classes, and the 3D classification and refinement workflow. The scale bar on the micrograph equates to 40.5 nm. b, An orientation distribution map of the particles used to reconstruct the final map. c, Local resolution estimation calculated by ResMap. d, Post-processing analysis. The masked (blue) and unmasked (red) Fourier shell correlation (FSC) curves of two half maps (top), map vs. model (bottom). e, Representative zoom-in views of the cryo-EM density in different conserved regions fitted with molecular models.
Extended Data Fig. 6 Single-particle analysis on rat GluN1-2B NMDAR in apo/glu state.
a, A representative EM micrograph, 2D classes, and the 3D classification and refinement workflow. The scale bar on the micrograph equates to 40.5 nm. b, An orientation distribution map of the particles used to reconstruct the final map. c, Local resolution estimation calculated by ResMap. d, Post-processing analysis. The masked (blue) and unmasked (red) Fourier shell correlation (FSC) curves of two half maps (top), map vs. model (bottom). e, Representative zoom-in views of the cryo-EM density in different conserved regions fitted with molecular models.
Extended Data Fig. 7 Structural comparisons between apo and pre-active states.
a, Cartoon representation of GluN1-2B NMDAR in the apo/apo state. The GluN1-2B ATD heterodimer and the channel gate are highlighted with dotted lines. b, A top-down view of the channel gate in the open, apo/apo, gly/apo, and apo/glu states. The gate residues are shown in spheres. c, Structural comparisons of GluN1-2B ATD heterodimers in different functional states. Distances between the GluN1 α5 and GluN2B α4′ in each state are shown for each functional state. d, Measurement of the central pore radii of the apo/apo, gly/apo, and apo/glu state structures.
Extended Data Fig. 8 Structural comparisons of GluN1-2B NMDAR in gly/apo and apo/glu states with apo/apo state.
a, Superposition of the gly/apo and apo/apo structures at GluN2B D2 (lower lobe) and GluN1 D1 (upper lobe) demonstrates no change in the bi-lobe orientation for GluN2B LBD and an 8.1° domain closure for GluN1 LBD (single-line arrow) in the gly/apo state. b, The GluN1 LBD bi-lobe closure is coupled to the 4° upward rotational movement of GluN1-2B LBD dimers relative to the membrane plane from the apo/apo to gly/apo (double-line arrows). c-d, These rotational movements are insufficient to create tension in the GluN2B LBD-M3′ linker for channel gating as measured by the distance between the GluN2B Gln662 residues. e, Superposition of the apo/glu and apo/apo structures at GluN2B D2 (lower lobe) and GluN1 D1 (upper lobe) displays 16.1° closure of the GluN2B LBD bi-lobe and 10.7° opening of the GluN1 LBD bi-lobe compared to the apo/apo state. f, These LBD bi-lobe movements are coupled to an 8° downward rotational movement relative to the membrane plane compared to the apo/apo state (double-line arrows). g-h, The GluN2B LBD-M3′ linkers in the apo/glu state do not have sufficient tension for channel gating as in the gly/apo and apo/apo states. Asterisks indicate the location of the D2 loop.
Supplementary information
Supplementary Methods
Chemicals and Synthesis of EU-1622-240.
Supplementary Video 1
Conformation transition from pre-active to open state. A substantial rotational movement of the extracellular domain relative to the TMD channel characterizes the shift from the pre-active to the open state. This dynamic process results in the bending of the GluN2B M3′ helices and the rotation of the GluN1 M3 helices. Such movements facilitate the repositioning of hydrophobic residues, effectively clearing the entrance of the channel gate and enabling ion passage. There is only a minor change in the ATD.
Supplementary Video 2
Conformation transition from gly/apo to pre-active state. The transition from the gly/apo to the pre-active state is marked by the closing of the GluN2B LBD bi-lobes. This action increases the tension of the GluN2B LBD–M3′ linker, which initiates a partial repositioning of the hydrophobic residues at the entrance of the channel gate (pre-active state). Therefore, the lack of the GluN2B LBD–M3′ linker tension in the absence of glutamate ensures that the NMDAR channel gate remains closed.
Supplementary Video 3
Conformation transition from apo/glu to pre-active state. The progression from the apo/glu to the pre-active state is marked by an upward rotation of the GluN1-2B LBD dimers, moving them away from the membrane plane. This movement, distinct from the transition from the gly/apo to the pre-active state (Supplementary Video 2), amplifies tension in the GluN2B LBD–M3′ linker. Conversely, the absence of glycine results in a downward rotation of the GluN1-2B LBDs towards the membrane plane, reducing the tension in the GluN2B LBD–M3′ linker and thus ensuring that the NMDAR channel gate remains closed, even in the presence of glutamate.
Supplementary Video 4
Scheme of ligand-gating and desensitization. The transition through apo/apo, gly/apo, pre-active, open, and non-active1 states is orchestrated by the extracellular domain movement, triggered by ligand bindings to the LBDs. These interactions control tension in the GluN2B LBD–M3′ linkers and the rotation of the LBDs relative to the TMD channel for the gate opening. The tension reduction in the GluN2B LBD–M3′ linkers through the rotation of the GluN1-2B LBD dimer bound to glycine and glutamate probably represents a transition to a desensitized state (non-active1). These dynamics are allosterically coupled to the ATD, demonstrating the interplay between various receptor domains regulating the channel functions.
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Chou, TH., Epstein, M., Fritzemeier, R.G. et al. Molecular mechanism of ligand gating and opening of NMDA receptor. Nature 632, 209–217 (2024). https://doi.org/10.1038/s41586-024-07742-0
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DOI: https://doi.org/10.1038/s41586-024-07742-0
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