5TQ2

Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A in complex with zinc at GluN1 and GluN2A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.289 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular Basis for Subtype Specificity and High-Affinity Zinc Inhibition in the GluN1-GluN2A NMDA Receptor Amino-Terminal Domain.

Romero-Hernandez, A.Simorowski, N.Karakas, E.Furukawa, H.

(2016) Neuron 92: 1324-1336

  • DOI: 10.1016/j.neuron.2016.11.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Zinc is vastly present in the mammalian brain and controls functions of various cell surface receptors to regulate neurotransmission. A distinctive characteristic of N-methyl-D-aspartate (NMDA) receptors containing a GluN2A subunit is that their ion ...

    Zinc is vastly present in the mammalian brain and controls functions of various cell surface receptors to regulate neurotransmission. A distinctive characteristic of N-methyl-D-aspartate (NMDA) receptors containing a GluN2A subunit is that their ion channel activity is allosterically inhibited by a nano-molar concentration of zinc that binds to an extracellular domain called an amino-terminal domain (ATD). Despite physiological importance, the molecular mechanism underlying the high-affinity zinc inhibition has been incomplete because of the lack of a GluN2A ATD structure. Here we show the first crystal structures of the heterodimeric GluN1-GluN2A ATD, which provide the complete map of the high-affinity zinc-binding site and reveal distinctive features from the ATD of the GluN1-GluN2B subtype. Perturbation of hydrogen bond networks at the hinge of the GluN2A bi-lobe structure affects both zinc inhibition and open probability, supporting the general model in which the bi-lobe motion in ATD regulates the channel activity in NMDA receptors.


    Organizational Affiliation

    WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor, NY 11724, USA. Electronic address: furukawa@cshl.edu.,WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor, NY 11724, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NMDA glutamate receptor subunit
A
389Xenopus laevisMutation(s): 2 
Gene Names: grin1
Find proteins for A0A1L8F5J9 (Xenopus laevis)
Go to UniProtKB:  A0A1L8F5J9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, NMDA 2A
B
360Rattus norvegicusMutation(s): 0 
Gene Names: Grin2a
Find proteins for Q00959 (Rattus norvegicus)
Go to UniProtKB:  Q00959
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FAB, HEAVY CHAIN
H
221N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
FAB, LIGHT CHAIN
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.289 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.163α = 90.00
b = 117.826β = 90.00
c = 158.992γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Refinement description
  • Version 1.2: 2018-05-16
    Type: Data collection, Database references
  • Version 1.3: 2019-11-27
    Type: Author supporting evidence