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Structure paper

TitleStructural basis for channel gating and blockade in tri-heteromeric GluN1-2B-2D NMDA receptor.
Journal, issue, pagesNeuron, Vol. 113, Issue 7, Page 991-1005.e5, Year 2025
Publish dateApr 2, 2025
AuthorsHyunook Kang / Max Epstein / Tue G Banke / Riley Perszyk / Noriko Simorowski / Srinu Paladugu / Dennis C Liotta / Stephen F Traynelis / Hiro Furukawa /
PubMed AbstractDiscrete activation of N-methyl-D-aspartate receptor (NMDAR) subtypes by glutamate and the co-agonist glycine is fundamental to neuroplasticity. A distinct variant, the tri-heteromeric receptor, ...Discrete activation of N-methyl-D-aspartate receptor (NMDAR) subtypes by glutamate and the co-agonist glycine is fundamental to neuroplasticity. A distinct variant, the tri-heteromeric receptor, comprising glycine-binding GluN1 and two types of glutamate-binding GluN2 subunits, exhibits unique pharmacological characteristics, notably enhanced sensitivity to the anti-depressant channel blocker S-(+)-ketamine. Despite its significance, the structural mechanisms underlying ligand gating and channel blockade of tri-heteromeric NMDARs remain poorly understood. Here, we identify and characterize tri-heteromeric GluN1-2B-2D NMDAR in the adult brain, resolving its structures in the activated, inhibited, and S-(+)-ketamine-blocked states. These structures reveal the ligand-dependent conformational dynamics that modulate the tension between the extracellular domain and transmembrane channels, governing channel gating and blockade. Additionally, we demonstrate that the inhibitor (S)-DQP-997-74 selectively decouples linker tension in GluN2D, offering insights into subtype-selective targeting for cognitive modulation.
External linksNeuron / PubMed:39954679 / PubMed Central
MethodsEM (single particle)
Resolution3.34 - 3.96 Å
Structure data

46526

9d37

EMDB-46526, PDB-9d37:
Nonactive state of Gly-,Glu- bound GluN1a-2B-2D NMDAR
Method: EM (single particle) / Resolution: 3.34 Å

46527

9d38

EMDB-46527, PDB-9d38:
Open state of Gly-,Glu-,EU1622-240 bound GluN1a-2B-2D NMDAR
Method: EM (single particle) / Resolution: 3.95 Å

46528

9d39

EMDB-46528, PDB-9d39:
Gly-,PPDA- bound GluN1a-2B-2D NMDAR
Method: EM (single particle) / Resolution: 3.65 Å

46529

9d3a

EMDB-46529, PDB-9d3a:
Nonactive state of Gly-,Glu- bound GluN1a-2B-2D NMDAR (Low-res)
Method: EM (single particle) / Resolution: 3.78 Å

46530

9d3b

EMDB-46530, PDB-9d3b:
Gly-,Glu-,(S)-DQP-997-74 bound GluN1a-2B-2D NMDAR
Method: EM (single particle) / Resolution: 3.71 Å

46531

9d3c

EMDB-46531, PDB-9d3c:
Gly-,Glu-,(S)-(+)-ketamine bound GluN1a-2B-2D NMDAR
Method: EM (single particle) / Resolution: 3.96 Å

Chemicals

ChemComp-GLY:
GLYCINE

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

ChemComp-GLU:
GLUTAMIC ACID

ChemComp-HOH:
WATER

ChemComp-2JL:
(2S,3R)-1-(phenanthren-2-ylcarbonyl)piperazine-2,3-dicarboxylic acid

PDB-1a15:
SDF-1ALPHA

ChemComp-JC9:
(2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one

Source
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / N-methyl-D-aspartate receptor / nonactive / GluN2B / GluN2D / open / NMDAR / PPDA-bound / (S)-DQP-997-74 / (S)-(+)-ketamine

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