5UN1

Crystal structure of GluN1/GluN2B delta-ATD NMDA receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.288 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of NMDA receptor channel block by MK-801 and memantine.

Song, X.Jensen, M.O.Jogini, V.Stein, R.A.Lee, C.H.Mchaourab, H.S.Shaw, D.E.Gouaux, E.

(2018) Nature 556: 515-519

  • DOI: 10.1038/s41586-018-0039-9

  • PubMed Abstract: 
  • The NMDA (N-methyl-D-aspartate) receptor transduces the binding of glutamate and glycine, coupling it to the opening of a calcium-permeable ion channel <sup>1 </sup> . Owing to the lack of high-resolution structural studies of the NMDA receptor, the ...

    The NMDA (N-methyl-D-aspartate) receptor transduces the binding of glutamate and glycine, coupling it to the opening of a calcium-permeable ion channel 1 . Owing to the lack of high-resolution structural studies of the NMDA receptor, the mechanism by which ion-channel blockers occlude ion permeation is not well understood. Here we show that removal of the amino-terminal domains from the GluN1-GluN2B NMDA receptor yields a functional receptor and crystals with good diffraction properties, allowing us to map the binding site of the NMDA receptor blocker, MK-801. This crystal structure, together with long-timescale molecular dynamics simulations, shows how MK-801 and memantine (a drug approved for the treatment of Alzheimer's disease) bind within the vestibule of the ion channel, promote closure of the ion channel gate and lodge between the M3-helix-bundle crossing and the M2-pore loops, physically blocking ion permeation.


    Organizational Affiliation

    D. E. Shaw Research, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. David.Shaw@DEShawResearch.com.,Howard Hughes Medical Institute, Oregon Health & Science University, Portland, OR, USA. gouauxe@ohsu.edu.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.,Vollum Institute, Oregon Health & Science University, Portland, OR, USA. gouauxe@ohsu.edu.,Vollum Institute, Oregon Health & Science University, Portland, OR, USA.,D. E. Shaw Research, New York, NY, USA. David.Shaw@DEShawResearch.com.,Rockefeller University, New York, NY, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-methyl-D-aspartate receptor subunit NR1-3a
G, A, E, C
451Xenopus laevisMutation(s): 0 
Gene Names: grin1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
GluN1a/GluN2B NMDA receptor
Find proteins for A0A1L8F5J9 (Xenopus laevis)
Go to UniProtKB:  A0A1L8F5J9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ionotropic glutamate receptor subunit NR2B
B, H, F, D
448Xenopus laevisMutation(s): 0 
Gene Names: grin2b
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
GluN1a/GluN2B NMDA receptor
Find proteins for A7XY94 (Xenopus laevis)
Go to UniProtKB:  A7XY94
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Y01
Query on Y01

Download SDF File 
Download CCD File 
E
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
 Ligand Interaction
GLY
Query on GLY

Download SDF File 
Download CCD File 
A, G
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
BMK
Query on BMK

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Download CCD File 
B, G
(5S,10R)-5-methyl-10,11-dihydro-5H-5,10-epiminodibenzo[a,d][7]annulene
C16 H15 N
LBOJYSIDWZQNJS-CVEARBPZSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GLU
Query on GLU

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Download CCD File 
B, D, G, H
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
B, D, F, G, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
TRS
Query on TRS

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Download CCD File 
G
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.288 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 181.570α = 90.00
b = 108.470β = 111.44
c = 182.460γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-01-30 
  • Released Date: 2018-02-07 
  • Deposition Author(s): Song, X., Gouaux, E.

Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references
  • Version 1.2: 2018-05-02
    Type: Data collection, Database references