4U4F

Structure of GluA2* in complex with partial agonist (S)-5-Nitrowillardiine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.79 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

Structure of an agonist-bound ionotropic glutamate receptor.

Yelshanskaya, M.V.Li, M.Sobolevsky, A.I.

(2014) Science 345: 1070-1074

  • DOI: 10.1126/science.1256508
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ionotropic glutamate receptors (iGluRs) mediate most excitatory neurotransmission in the central nervous system and function by opening their ion channel in response to binding of agonist glutamate. Here, we report a structure of a homotetrameric rat ...

    Ionotropic glutamate receptors (iGluRs) mediate most excitatory neurotransmission in the central nervous system and function by opening their ion channel in response to binding of agonist glutamate. Here, we report a structure of a homotetrameric rat GluA2 receptor in complex with partial agonist (S)-5-nitrowillardiine. Comparison of this structure with the closed-state structure in complex with competitive antagonist ZK 200775 suggests conformational changes that occur during iGluR gating. Guided by the structures, we engineered disulfide cross-links to probe domain interactions that are important for iGluR gating events. The combination of structural information, kinetic modeling, and biochemical and electrophysiological experiments provides insight into the mechanism of iGluR gating.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY 10032, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
A, B, C, D
822Rattus norvegicusMutation(s): 0 
Gene Names: Gria2 (Glur2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
GluA2 Glutamate receptor (AMPA-subtype)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NWD
Query on NWD

Download SDF File 
Download CCD File 
A, B, C, D
3-(5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine
nitrowillardiine
C7 H8 N4 O6
IEBVITXSHAFLJR-VKHMYHEASA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.79 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.228 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 141.374α = 90.00
b = 166.575β = 90.00
c = 566.604γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited StatesNS083660

Revision History 

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references
  • Version 2.0: 2017-09-13
    Type: Atomic model, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 2.1: 2017-11-22
    Type: Refinement description