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

Experimental Data Snapshot

  • 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 2.0 of the entry. See complete history


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: https://doi.org/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). 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

    Program in Cellular Regulation and Metabolism, NICHD, NIH, Bethesda, MD 20892, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
268Drosophila melanogasterMutation(s): 0 
Gene Names: CG3822Dmel_CG3822
Find proteins for Q8MS48 (Drosophila melanogaster)
Explore Q8MS48 
Go to UniProtKB:  Q8MS48
Find proteins for Q9VDH5 (Drosophila melanogaster)
Explore Q9VDH5 
Go to UniProtKB:  Q9VDH5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ8MS48Q9VDH5
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.891α = 90
b = 56.891β = 90
c = 143.584γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

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
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection