5B3J

Activation of NMDA receptors and the mechanism of inhibition by ifenprodil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.275 

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This is version 1.6 of the entry. See complete history


Literature

Activation of NMDA receptors and the mechanism of inhibition by ifenprodil

Tajima, N.Karakas, E.Grant, T.Simorowski, N.Diaz-Avalos, R.Grigorieff, N.Furukawa, H.

(2016) Nature 534: 63-68

  • DOI: https://doi.org/10.1038/nature17679
  • Primary Citation of Related Structures:  
    5B3J, 5FXG, 5FXH, 5FXI, 5FXJ, 5FXK

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Cold Spring Harbor Laboratory, W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York 11724, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NMDA glutamate receptor subunit
A, B
383Xenopus laevisMutation(s): 2 
Gene Names: grin1NR1
Membrane Entity: Yes 
UniProt
Find proteins for A0A1L8F5J9 (Xenopus laevis)
Explore A0A1L8F5J9 
Go to UniProtKB:  A0A1L8F5J9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L8F5J9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2BC,
E [auth D]
364Rattus norvegicusMutation(s): 1 
Gene Names: Grin2b
Membrane Entity: Yes 
UniProt
Find proteins for Q00960 (Rattus norvegicus)
Explore Q00960 
Go to UniProtKB:  Q00960
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UniProt GroupQ00960
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab, heavy chainD [auth E],
G [auth H]
224Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab, light chainF,
H [auth L]
213Mus musculusMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.275 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 247.249α = 90
b = 79.903β = 127.09
c = 181.314γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHENIXdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesMH085926
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM105730

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2016-05-18
    Changes: Database references
  • Version 1.2: 2016-06-15
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2017-10-18
    Changes: Author supporting evidence
  • Version 1.5: 2022-03-23
    Changes: Author supporting evidence, Database references
  • Version 1.6: 2024-10-23
    Changes: Data collection, Structure summary