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TitleCryo-EM snapshots of NMDA receptor activation illuminate sequential rearrangements.
Journal, issue, pagesSci Adv, Vol. 11, Issue 39, Page eadx4647, Year 2025
Publish dateSep 26, 2025
AuthorsJamie A Abbott / Junhoe Kim / Beiying Liu / Gabriela K Popescu / Eric Gouaux / Farzad Jalali-Yazdi /
PubMed AbstractCanonical -methyl-d-aspartate receptors (NMDARs) are glutamate-gated ion channels with critical roles in the development and function of the nervous system. The excitatory currents they produce ...Canonical -methyl-d-aspartate receptors (NMDARs) are glutamate-gated ion channels with critical roles in the development and function of the nervous system. The excitatory currents they produce reflect stochastic transitions between multiple agonist-bound closed- and open-pore states. We leveraged the intrinsically high open probability () of NMDARs composed of GluN1 and GluN2A subunits, together with judiciously chosen mutants and ligands, to achieve conditions in which receptors had a near unity. Using single-particle cryo-electron microscopy (cryo-EM), we captured three activated receptor states, each with distinct conformations of the gate-forming M3 helices. Separately, we carried out single-channel electrophysiology, together with statistical modeling, to relate the cryo-EM structures to the gating reaction. NMDAR channel opening involves bending of the pore-forming M3 helices to produce a transient open-channel conformation, subsequently stabilized by new interactions between the D2-M3 linkers with the pre-M1 helices and the pre-M4 loops, to yield the stable open channel.
External linksSci Adv / PubMed:40991709 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 4.61 Å
Structure data

45279

9c7c

9c7e

EMDB-45279, PDB-9c7c:
Diheteromeric GluN1/GluN2A (delM653) in nanodisc complexed with glycine, glutamate, and GNE-4123, open conformation
PDB-9c7e: Diheteromeric GluN1/GluN2A (delM653) in nanodisc complex with glycine, glutamate, and GNE-4123, open conformation, C2 symmetry
Method: EM (single particle) / Resolution: 3.1 Å

45283

9c7p

EMDB-45283, PDB-9c7p:
Diheteromeric GluN1/GluN2A (delM653) in digitonin complexed with glycine, glutamate, and GNE-4123
Method: EM (single particle) / Resolution: 4.61 Å

45284

9c7q

EMDB-45284: Diheteromeric GluN1/GluN2A (delM653) in digitonin complexed with glycine and glutamate
PDB-9c7q: Diheteromeric NMDA receptor GluN1/GluN2A, in complex with glycine and glutamate
Method: EM (single particle) / Resolution: 4.05 Å

45285

9c7r

EMDB-45285, PDB-9c7r:
Diheteromeric GluN1/GluN2A (M817V) in digitonin complexed with glycine, glutamate, and GNE-4123
Method: EM (single particle) / Resolution: 3.99 Å

Chemicals

PDB-1auv:
STRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN

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

ChemComp-HP6:
HEPTANE

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

ChemComp-GLY:
GLYCINE

ChemComp-D12:
DODECANE

ChemComp-GLU:
GLUTAMIC ACID

ChemComp-D10:
DECANE

ChemComp-HEX:
HEXANE

Source
  • rattus norvegicus (Norway rat)
  • aequorea victoria (jellyfish)
KeywordsTRANSPORT PROTEIN / ion channel / NMDA / positive allosteric modulator / open pore conformation / pre-open pore conformation

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