6UZR | pdb_00006uzr

Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and homoquinolinic acid

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Rattus norvegicus
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2019-11-15 Released: 2020-01-29 
  • Deposition Author(s): Wang, J.X., Furukawa, H.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.207 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6UZR

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural basis of subtype-selective competitive antagonism for GluN2C/2D-containing NMDA receptors.

Wang, J.X.Irvine, M.W.Burnell, E.S.Sapkota, K.Thatcher, R.J.Li, M.Simorowski, N.Volianskis, A.Collingridge, G.L.Monaghan, D.T.Jane, D.E.Furukawa, H.

(2020) Nat Commun 11: 423-423

  • DOI: https://doi.org/10.1038/s41467-020-14321-0
  • Primary Citation Related Structures: 
    6UZ6, 6UZG, 6UZR, 6UZW, 6UZX

  • PubMed Abstract: 

    N-Methyl-D-aspartate receptors (NMDARs) play critical roles in the central nervous system. Their heterotetrameric composition generates subtypes with distinct functional properties and spatio-temporal distribution in the brain, raising the possibility for subtype-specific targeting by pharmacological means for treatment of neurological diseases. While specific compounds for GluN2A and GluN2B-containing NMDARs are well established, those that target GluN2C and GluN2D are currently underdeveloped with low potency and uncharacterized binding modes. Here, using electrophysiology and X-ray crystallography, we show that UBP791 ((2S*,3R*)-1-(7-(2-carboxyethyl)phenanthrene-2-carbonyl)piperazine-2,3-dicarboxylic acid) inhibits GluN2C/2D with 40-fold selectivity over GluN2A-containing receptors, and that a methionine and a lysine residue in the ligand binding pocket (GluN2D-Met763/Lys766, GluN2C-Met736/Lys739) are the critical molecular elements for the subtype-specific binding. These findings led to development of UBP1700 ((2S*,3R*)-1-(7-(2-carboxyvinyl)phenanthrene-2-carbonyl)piperazine-2,3-dicarboxylic acid) which shows over 50-fold GluN2C/2D-selectivity over GluN2A with potencies in the low nanomolar range. Our study shows that the L-glutamate binding site can be targeted for GluN2C/2D-specific inhibition.


  • Organizational Affiliation
    • WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.

Macromolecule Content 

  • Total Structure Weight: 65.57 kDa 
  • Atom Count: 4,987 
  • Modeled Residue Count: 566 
  • Deposited Residue Count: 574 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 1292Rattus norvegicusMutation(s): 0 
Gene Names: Grin1Nmdar1
UniProt
Find proteins for P35439 (Rattus norvegicus)
Explore P35439 
Go to UniProtKB:  P35439
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35439
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2A282Rattus norvegicusMutation(s): 0 
Gene Names: Grin2a
UniProt
Find proteins for Q00959 (Rattus norvegicus)
Explore Q00959 
Go to UniProtKB:  Q00959
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00959
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.207 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.367α = 90
b = 88.717β = 90
c = 125.483γ = 90
Software Package:
Software NamePurpose
autoPROCdata collection
XDSdata reduction
Aimlessdata scaling
pointlessdata scaling
REFMACphasing
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS111745
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesMH085926

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary