4JWX | pdb_00004jwx

GluN2A ligand-binding core in complex with propyl-NHP5G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.195 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4JWX

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural determinants of agonist efficacy at the glutamate binding site of N-methyl-d-aspartate receptors.

Hansen, K.B.Tajima, N.Risgaard, R.Perszyk, R.E.Jorgensen, L.Vance, K.M.Ogden, K.K.Clausen, R.P.Furukawa, H.Traynelis, S.F.

(2013) Mol Pharmacol 84: 114-127

  • DOI: https://doi.org/10.1124/mol.113.085803
  • Primary Citation Related Structures: 
    4JWX, 4JWY

  • PubMed Abstract: 

    N-methyl-d-aspartate (NMDA) receptors are ligand-gated ion channels assembled from GluN1 and GluN2 subunits. We used a series of N-hydroxypyrazole-5-glycine (NHP5G) partial agonists at the GluN2 glutamate binding site as tools to study activation of GluN1/GluN2A and GluN1/GluN2D NMDA receptor subtypes. Using two-electrode voltage-clamp electrophysiology, fast-application patch-clamp, and single-channel recordings, we show that propyl- and ethyl-substituted NHP5G agonists have a broad range of agonist efficacies relative to the full agonist glutamate (<1-72%). Crystal structures of the agonist binding domains (ABDs) of GluN2A and GluN2D do not reveal any differences in the overall domain conformation induced by binding of the full agonist glutamate or the partial agonist propyl-NHP5G, which is strikingly different from ABD structures of 2-amino-3-(3-hydroxy-5-methylisoxazol-4-yl)propanoate (AMPA) and kainate receptors bound to full and partial agonists. Subsequent evaluation of relative NHP5G agonist efficacy at GluN2A-GluN2D chimeric subunits implicates the amino-terminal domain (ATD) as a strong determinant of agonist efficacy, suggesting that interdomain interactions between the ABD and the ATD may be a central element in controlling the manner by which agonist binding leads to channel opening. We propose that variation in the overall receptor conformation, which is strongly influenced by the nature of interdomain interactions in resting and active states, mediates differences in agonist efficacy and partial agonism at the GluN2 subunits.


  • Organizational Affiliation
    • Department of Pharmacology, Emory University School of Medicine, 1510 Clifton Road, Rollins Research Center, Atlanta, GA 30322, USA.

Macromolecule Content 

  • Total Structure Weight: 31.62 kDa 
  • Atom Count: 2,844 
  • Modeled Residue Count: 280 
  • Deposited Residue Count: 280 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GluN2A280Rattus norvegicusMutation(s): 0 
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

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1N4

Query on 1N4



Download:Ideal Coordinates CCD File
B [auth A](2R)-amino(1-hydroxy-4-propyl-1H-pyrazol-5-yl)ethanoic acid
C8 H13 N3 O3
SSPXLOGHCJIQFQ-ZCFIWIBFSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.195 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.031α = 90
b = 52.031β = 90
c = 198.823γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary