4GPA

High resolution structure of the GluA4 N-terminal domain (NTD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Comparative Dynamics of NMDA- and AMPA-Glutamate Receptor N-Terminal Domains.

Dutta, A.Shrivastava, I.H.Sukumaran, M.Greger, I.H.Bahar, I.

(2012) Structure 20: 1838-1849

  • DOI: 10.1016/j.str.2012.08.012

  • PubMed Abstract: 
  • Ionotropic glutamate receptors (iGluRs) harbor two¬†extracellular domains: the membrane-proximal ligand-binding domain (LBD) and the distal N-terminal domain (NTD). These are involved in signal sensing: the LBD binds L-glutamate, which activates the r ...

    Ionotropic glutamate receptors (iGluRs) harbor two extracellular domains: the membrane-proximal ligand-binding domain (LBD) and the distal N-terminal domain (NTD). These are involved in signal sensing: the LBD binds L-glutamate, which activates the receptor channel. Ligand binding to the NTD modulates channel function in the NMDA receptor subfamily of iGluRs, which has not been observed for the AMPAR subfamily to date. Structural data suggest that AMPAR NTDs are packed into tight dimers and have lost their signaling potential. Here, we assess NTD dynamics from both subfamilies, using a variety of computational tools. We describe the conformational motions that underly NMDAR NTD allosteric signaling. Unexpectedly, AMPAR NTDs are capable of undergoing similar dynamics; although dimerization imposes restrictions, the two subfamilies sample similar, interconvertible conformational subspaces. Finally, we solve the crystal structure of AMPAR GluA4 NTD, and combined with molecular dynamics simulations, we characterize regions pivotal for an as-yet-unexplored dynamic spectrum of AMPAR NTDs.


    Organizational Affiliation

    Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 4
A
389Rattus norvegicusMutation(s): 0 
Gene Names: Gria4 (Glur4)
Find proteins for P19493 (Rattus norvegicus)
Go to UniProtKB:  P19493
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 2.25 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 104.540α = 90.00
b = 104.540β = 90.00
c = 108.980γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
ADSCdata collection
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Database references