5EHM

Crystal structure of the Drosophila CG3822 KaiR1D ligand binding domain complex with NMDA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Novel Functional Properties of Drosophila CNS Glutamate Receptors.

Li, Y., Dharkar, P., Han, T.H., Serpe, M., Lee, C.H., Mayer, M.L.

(2016) Neuron 92: 1036-1048

  • DOI: 10.1016/j.neuron.2016.10.058
  • Primary Citation of Related Structures:  
    5DT6, 5DTB, 5EHM, 5EHS, 5ICT

  • PubMed Abstract: 

    • Phylogenetic analysis reveals AMPA, kainate, and NMDA receptor families in insect genomes, suggesting conserved functional properties corresponding to their vertebrate counterparts. However, heterologous expression of the Drosophila kainate receptor DKaiR1D and the AMPA receptor DGluR1A revealed novel ligand selectivity at odds with the classification used for vertebrate glutamate receptor ion channels (iGluRs) ...

    Phylogenetic analysis reveals AMPA, kainate, and NMDA receptor families in insect genomes, suggesting conserved functional properties corresponding to their vertebrate counterparts. However, heterologous expression of the Drosophila kainate receptor DKaiR1D and the AMPA receptor DGluR1A revealed novel ligand selectivity at odds with the classification used for vertebrate glutamate receptor ion channels (iGluRs). DKaiR1D forms a rapidly activating and desensitizing receptor that is inhibited by both NMDA and the NMDA receptor antagonist AP5; crystallization of the KaiR1D ligand-binding domain reveals that these ligands stabilize open cleft conformations, explaining their action as antagonists. Surprisingly, the AMPA receptor DGluR1A shows weak activation by its namesake agonist AMPA and also by quisqualate. Crystallization of the DGluR1A ligand-binding domain reveals amino acid exchanges that interfere with binding of these ligands. The unexpected ligand-binding profiles of insect iGluRs allows classical tools to be used in novel approaches for the study of synaptic regulation. VIDEO ABSTRACT.

    Organizational Affiliation: 

    Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, NICHD, NIH, Bethesda, MD 20892, USA. Electronic address: mayerm@mail.nih.gov.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RE06730p,CG3822A, B268Drosophila melanogasterMutation(s): 0 
Gene Names: CG3822, Dmel_CG3822
UniProt
Find proteins for Q9VDH5 (Drosophila melanogaster)
Explore Q9VDH5 
Go to UniProtKB:  Q9VDH5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OEM
Query on OEM
Download Ideal Coordinates CCD File 
C [auth A], D [auth B]N-methyl-D-aspartic acid
C5 H9 N O4
HOKKHZGPKSLGJE-GSVOUGTGSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 31
  • Diffraction Data DOI: 10.15785/SBGRID/402 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.891α = 90
b = 56.891β = 90
c = 143.584γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references