9OOT

Pre-active state of Gly/Glu/Pregnenolone Sulfate bound hGluN1a-2B NMDAR

Summary for 9OOT

• Entry DOI: 10.2210/pdb9oot/pdb
• EMDB information: 70672
• Descriptor: Glutamate receptor ionotropic, NMDA 1, Glutamate receptor ionotropic, NMDA 2B, GLYCINE, ... (6 entities in total)
• Functional Keywords: n-methyl-d-aspartate receptor, pre-active, glun2b, pregnenolone sulfate, membrane protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 384157.09

Authors

Hyunook, K.,Hiro, F. (deposition date: 2025-05-16, release date: 2025-10-29, Last modification date: 2025-12-17)

Primary citation

Kang, H.,Steigerwald, R.,Ullman, E.Z.,Epstein, M.,Paladugu, S.,Liotta, D.C.,Traynelis, S.F.,Furukawa, H.
Mechanism of conductance control and neurosteroid binding in NMDA receptors.
Nature, 648:220-228, 2025

PubMed Abstract: Ion-channel activity reflects a combination of open probability and unitary conductance. Many channels display subconductance states that modulate signalling strength, yet the structural mechanisms governing conductance levels remain incompletely understood. Here we report that conductance levels are controlled by the bending patterns of pore-forming transmembrane helices in the heterotetrameric neuronal channel GluN1a-2B N-methyl-D-aspartate receptor (NMDAR). Our single-particle electron cryomicroscopy (cryo-EM) analyses demonstrate that an endogenous neurosteroid and synthetic positive allosteric modulator (PAM), 24S-hydroxycholesterol (24S-HC), binds to a juxtamembrane pocket in the GluN2B subunit and stabilizes the fully open-gate conformation, where GluN1a M3 and GluN2B M3' pore-forming helices are bent to dilate the channel pore. By contrast, EU1622-240 binds to the same GluN2B juxtamembrane pocket and a distinct juxtamembrane pocket in GluN1a to stabilize a sub-open state whereby only the GluN2B M3' helix is bent. Consistent with the varying extents of gate opening, the single-channel recordings predominantly show full-conductance and subconductance states in the presence of 24S-HC and EU1622-240, respectively. Another class of neurosteroid, pregnenolone sulfate, engages a similar GluN2B pocket, but two molecules bind simultaneously, revealing a diverse neurosteroid recognition pattern. Our study identifies that the juxtamembrane pockets are critical structural hubs for modulating conductance levels in NMDAR.

PubMed: 41162707
DOI: 10.1038/s41586-025-09695-4

Experimental method

ELECTRON MICROSCOPY (3.13 Å)