Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.97 kDa 
• Atom Count: 5046 
• Residue Count: 518 
• Unique protein chains: 1

5EHM

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

• DOI: 10.2210/pdb5EHM/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-28 Released: 2016-11-09 
• Deposition Author(s): Dharkar, P., Mayer, M.L.

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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 

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

• PubMed: 27889096 
• DOI: 10.1016/j.neuron.2016.10.058
• Primary Citation of Related Structures:  
  5DTB, 5DT6, 5EHS, 5EHM, 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.

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Organizational Affiliation: 

Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, NICHD, NIH, Bethesda, MD 20892, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RE06730p,CG3822	A, B	268	Drosophila melanogaster	Mutation(s): 0  Gene Names: CG3822
Find proteins for Q9VDH5 (Drosophila melanogaster) Explore Q9VDH5  Go to UniProtKB:  Q9VDH5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OEM	A, B	N-methyl-D-aspartic acid C5 H9 N O4 HOKKHZGPKSLGJE-GSVOUGTGSA-N

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 = 56.891	α = 90
b = 56.891	β = 90
c = 143.584	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-10-28 
• Released Date: 2016-11-09 
Deposition Author(s): Dharkar, P., Mayer, M.L.

Revision History 

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