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TitleMolecular mechanism of ligand gating and opening of NMDA receptor.
Journal, issue, pagesNature, Vol. 632, Issue 8023, Page 209-217, Year 2024
Publish dateJul 31, 2024
AuthorsTsung-Han Chou / Max Epstein / Russell G Fritzemeier / Nicholas S Akins / Srinu Paladugu / Elijah Z Ullman / Dennis C Liotta / Stephen F Traynelis / Hiro Furukawa /
PubMed AbstractGlutamate transmission and activation of ionotropic glutamate receptors are the fundamental means by which neurons control their excitability and neuroplasticity. The N-methyl-D-aspartate receptor ...Glutamate transmission and activation of ionotropic glutamate receptors are the fundamental means by which neurons control their excitability and neuroplasticity. 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, respectively. 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.
External linksNature / PubMed:39085540 / PubMed Central
MethodsEM (single particle)
Resolution3.13 - 4.05 Å
Structure data

EMDB-43779, PDB-9are:
Rat GluN1-GluN2B NMDA receptor channel in complex with glycine, glutamate, and EU-1622-A, in open-channel conformation
Method: EM (single particle) / Resolution: 3.72 Å

EMDB-43780, PDB-9arf:
Rat GluN1-GluN2B NMDA receptor channel in complex with glycine, glutamate, and EU-1622-A, in nonactive1 conformation
Method: EM (single particle) / Resolution: 3.13 Å

EMDB-43781, PDB-9arg:
Rat GluN1-GluN2B NMDA receptor channel in apo conformation
Method: EM (single particle) / Resolution: 4.05 Å

EMDB-43782, PDB-9arh:
Rat GluN1-GluN2B NMDA receptor channel in complex with glycine
Method: EM (single particle) / Resolution: 3.69 Å

EMDB-43783, PDB-9ari:
Rat GluN1-GluN2B NMDA receptor channel in complex with glutamate
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-44586, PDB-9bib:
Rat GluN1-GluN2B NMDA receptor channel in complex with glycine, glutamate, and EU-1622-A, in open-channel conformation, C1 symmetry
Method: EM (single particle) / Resolution: 3.81 Å

Chemicals

ChemComp-GLY:
GLYCINE

ChemComp-GLU:
GLUTAMIC ACID

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

Source
  • rattus norvegicus (Norway rat)
KeywordsMEMBRANE PROTEIN / Ligand-gated ion channel / ionotropic glutamate receptor / synaptic membrane protein / Ion channel

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