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bioRxiv · 10.1101/2022.11.09.514853

Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits

Zhang, J.·Zhang, M.·Wang, Q.·Wen, H.·Liu, Z.·Wang, F.·Wang, Y.·Yao, F.·Song, N.·Kou, Z.·Li, Y.·Guo, F.·ZHU, S.
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Abstract

N-Methyl-D-Aspartate (NMDA) receptors are essential for many brain functions. These receptors are heterotetramers typically comprising two GluN1 subunits and two GluN2 subunits. The latter could alternate among four subtypes (N2A-N2D) and determine the functional diversity of NMDA receptors1, 2. For example, receptors containing N2C or N2D exhibit 50-fold lower channel open probability (Po) than those containing N2A (ref.3-5). Structures of N2A- and N2B-containing receptors have been extensively characterized, providing molecular basis for understanding NMDA receptor function6-14. Here we report the cryo-EM structures of N1-N2D and N1-N2C di-heterotetramers (di-receptors), and N1-N2A-N2C tri-heterotetramer (tri-receptor) at a resolution up to 3.0 [A]. Structural analysis showed that the bilobate N-terminal domain (NTD) in N2D adopted an intrinsic closed conformation, leading to a compact NTD tetramer in N1-N2D receptor. Functional studies further demonstrated that, in di-receptors containing N2D but not N2A or N2B, crosslinking NTD at the tetrameric interface had no effect on channel activity, while crosslinking ligand-binding domain (LBD) of two N1 protomers significantly elevated Po. Surprisingly, we found that the N1-N2C di-receptors spontaneously oscillated between symmetric and asymmetric conformation. The later one occupied a predominant population, whereby two N2C protomers exhibited distinct conformation. This asymmetry, which was also found to a lesser extent in N1-N2A di-receptor10, was further locked by the binding of an N2C-specific allosteric potentiator PYD-106 to a unique binding pocket between NTD and LBD in only one N2C protomer. Finally, N2A and N2C in the N1-N2A-N2C tri-receptor displayed the conformation close to that found in one protomer of N1-N2A and N1-N2C di-receptors, respectively. These findings provide a comprehensive structural understanding of diverse functional properties of major NMDA receptor subtypes.

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Zhang, J., Zhang, M., Wang, Q., Wen, H., Liu, Z., Wang, F., Wang, Y., Yao, F., Song, N., Kou, Z., Li, Y., Guo, F., ZHU, S.. 2022-11-10. Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits. https://doi.org/10.1101/2022.11.09.514853

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