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TitleActivation of NMDA receptors and the mechanism of inhibition by ifenprodil.
Journal, issue, pagesNature, Vol. 534, Issue 7605, Page 63-68, Year 2016
Publish dateJun 2, 2016
AuthorsNami Tajima / Erkan Karakas / Timothy Grant / Noriko Simorowski / Ruben Diaz-Avalos / Nikolaus Grigorieff / Hiro Furukawa /
PubMed AbstractThe physiology of N-methyl-d-aspartate (NMDA) receptors is fundamental to brain development and function. NMDA receptors are ionotropic glutamate receptors that function as heterotetramers composed ...The physiology of N-methyl-d-aspartate (NMDA) receptors is fundamental to brain development and function. NMDA receptors are ionotropic glutamate receptors that function as heterotetramers composed mainly of GluN1 and GluN2 subunits. Activation of NMDA receptors requires binding of neurotransmitter agonists to a ligand-binding domain (LBD) and structural rearrangement of an amino-terminal domain (ATD). Recent crystal structures of GluN1-GluN2B NMDA receptors bound to agonists and an allosteric inhibitor, ifenprodil, represent the allosterically inhibited state. However, how the ATD and LBD move to activate the NMDA receptor ion channel remains unclear. Here we applied X-ray crystallography, single-particle electron cryomicroscopy and electrophysiology to rat NMDA receptors to show that, in the absence of ifenprodil, the bi-lobed structure of GluN2 ATD adopts an open conformation accompanied by rearrangement of the GluN1-GluN2 ATD heterodimeric interface, altering subunit orientation in the ATD and LBD and forming an active receptor conformation that gates the ion channel.
External linksNature / PubMed:27135925 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.9 - 6.8 Å
Structure data

3352

5fxg

EMDB-3352: Activation of NMDA receptors and the mechanism of inhibition by ifenprodil - Active confirmation
PDB-5fxg: GLUN1B-GLUN2B NMDA RECEPTOR IN ACTIVE CONFORMATION
Method: EM (single particle) / Resolution: 6.8 Å

3353

5fxh

EMDB-3353: Activation of NMDA receptors and the mechanism of inhibition by ifenprodil - Non-Active 1 Conformation
PDB-5fxh: GluN1b-GluN2B NMDA receptor in non-active-1 conformation
Method: EM (single particle) / Resolution: 5.0 Å

3354

5fxi

EMDB-3354: Activation of NMDA receptors and the mechanism of inhibition by ifenprodil - Non-Active 2 confirmation
PDB-5fxi: GluN1b-GluN2B NMDA receptor structure in non-active-2 conformation
Method: EM (single particle) / Resolution: 5.5 Å

3355

5fxj

EMDB-3355: Activation of NMDA receptors and the mechanism of inhibition by ifenprodil - Class X
PDB-5fxj: GluN1b-GluN2B NMDA receptor structure-Class X
Method: EM (single particle) / Resolution: 6.25 Å

3356

5fxk

EMDB-3356: Activation of NMDA receptors and the mechanism of inhibition by ifenprodil - Class Y
PDB-5fxk: GluN1b-GluN2B NMDA receptor structure-Class Y
Method: EM (single particle) / Resolution: 6.25 Å

PDB-5b3j:
Activation of NMDA receptors and the mechanism of inhibition by ifenprodil
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

Chemicals

ChemComp-NA:
Unknown entry

ChemComp-HOH:
WATER

Source
  • rattus norvegicus (Norway rat)
  • xenopus laevis (African clawed frog)
  • mus musculus (house mouse)
KeywordsTRANSPORT PROTEIN / NMDA receptor / SIGNALING PROTEIN / GLUTAMATE RECEPTOR / GLUN1 / GLUN2B / ION CHANNEL

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