4IO3

Crystal Structure of the AvGluR1 ligand binding domain complex with aspartate at 1.66 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Anions Mediate Ligand Binding in Adineta vaga Glutamate Receptor Ion Channels.

Lomash, S.Chittori, S.Brown, P.Mayer, M.L.

(2013) Structure 21: 414-425

  • DOI: https://doi.org/10.1016/j.str.2013.01.006
  • Primary Citation of Related Structures:  
    4IO2, 4IO3, 4IO4, 4IO5, 4IO6, 4IO7

  • PubMed Abstract: 

    AvGluR1, a glutamate receptor ion channel from the primitive eukaryote Adineta vaga, is activated by alanine, cysteine, methionine, and phenylalanine, which produce lectin-sensitive desensitizing responses like those to glutamate, aspartate, and serine. AvGluR1 LBD crystal structures reveal an unusual scheme for binding dissimilar ligands that may be utilized by distantly related odorant/chemosensory receptors. Arginine residues in domain 2 coordinate the γ-carboxyl group of glutamate, whereas in the alanine, methionine, and serine complexes a chloride ion acts as a surrogate ligand, replacing the γ-carboxyl group. Removal of Cl(-) lowers affinity for these ligands but not for glutamate or aspartate nor for phenylalanine, which occludes the anion binding site and binds with low affinity. AvGluR1 LBD crystal structures and sedimentation analysis also provide insights into the evolutionary link between prokaryotic and eukaryotic iGluRs and reveal features unique to both classes, emphasizing the need for additional structure-based studies on iGluR-ligand interactions.


  • Organizational Affiliation

    Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development/NIH/DHHS, Bethesda, MD 20892, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AvGluR1 ligand binding domain
A, B
248Adineta vagaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E9P5T5 (Adineta vaga)
Explore E9P5T5 
Go to UniProtKB:  E9P5T5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9P5T5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.132α = 90
b = 100.364β = 116.4
c = 56.896γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-03-20
    Changes: Database references
  • Version 1.2: 2017-08-09
    Changes: Source and taxonomy
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description