6USV

Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and SDZ 220-040


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.3 of the entry. See complete history


Literature

Structural Basis of Functional Transitions in Mammalian NMDA Receptors.

Chou, T.H.Tajima, N.Romero-Hernandez, A.Furukawa, H.

(2020) Cell 182: 357

  • DOI: https://doi.org/10.1016/j.cell.2020.05.052
  • Primary Citation of Related Structures:  
    6USU, 6USV, 6WHR, 6WHS, 6WHT, 6WHU, 6WHV, 6WHW, 6WHX, 6WHY, 6WI0, 6WI1

  • PubMed Abstract: 

    Excitatory neurotransmission meditated by glutamate receptors including N-methyl-D-aspartate receptors (NMDARs) is pivotal to brain development and function. NMDARs are heterotetramers composed of GluN1 and GluN2 subunits, which bind glycine and glutamate, respectively, to activate their ion channels. Despite importance in brain physiology, the precise mechanisms by which activation and inhibition occur via subunit-specific binding of agonists and antagonists remain largely unknown. Here, we show the detailed patterns of conformational changes and inter-subunit and -domain reorientation leading to agonist-gating and subunit-dependent competitive inhibition by providing multiple structures in distinct ligand states at 4 Å or better. The structures reveal that activation and competitive inhibition by both GluN1 and GluN2 antagonists occur by controlling the tension of the linker between the ligand-binding domain and the transmembrane ion channel of the GluN2 subunit. Our results provide detailed mechanistic insights into NMDAR pharmacology, activation, and inhibition, which are fundamental to the brain physiology.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 1292Rattus norvegicusMutation(s): 0 
Gene Names: Grin1Nmdar1
Membrane Entity: Yes 
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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2A283Rattus norvegicusMutation(s): 0 
Gene Names: Grin2a
Membrane Entity: Yes 
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QGP (Subject of Investigation/LOI)
Query on QGP

Download Ideal Coordinates CCD File 
D [auth B](2S)-2-amino-3-[2',4'-dichloro-4-hydroxy-5-(phosphonomethyl)biphenyl-3-yl]propanoic acid
C16 H16 Cl2 N O6 P
NYZFUZCCDOSQBG-AWEZNQCLSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
GLY (Subject of Investigation/LOI)
Query on GLY

Download Ideal Coordinates CCD File 
C [auth A]GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.281α = 90
b = 85.131β = 90
c = 121.675γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)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: 2020-07-15
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary