2I3W

Measurement of conformational changes accompanying desensitization in an ionotropic glutamate receptor: Structure of S729C mutant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 

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This is version 1.3 of the entry. See complete history. 


Literature

Measurement of Conformational Changes accompanying Desensitization in an Ionotropic Glutamate Receptor.

Armstrong, N., Jasti, J., Beich-Frandsen, M., Gouaux, E.

(2006) Cell 127: 85-97

  • DOI: 10.1016/j.cell.2006.08.037
  • Primary Citation of Related Structures:  
    2I3W, 2I3V

  • PubMed Abstract: 

    • The canonical conformational states occupied by most ligand-gated ion channels, and many cell-surface receptors, are the resting, activated, and desensitized states. While the resting and activated states of multiple receptors are well characterized, ...

    The canonical conformational states occupied by most ligand-gated ion channels, and many cell-surface receptors, are the resting, activated, and desensitized states. While the resting and activated states of multiple receptors are well characterized, elaboration of the structural properties of the desensitized state, a state that is by definition inactive, has proven difficult. Here we use electrical, chemical, and crystallographic experiments on the AMPA-sensitive GluR2 receptor, defining the conformational rearrangements of the agonist binding cores that occur upon desensitization of this ligand-gated ion channel. These studies demonstrate that desensitization involves the rupture of an extensive interface between domain 1 of 2-fold related glutamate-binding core subunits, compensating for the ca. 21 degrees of domain closure induced by glutamate binding. The rupture of the domain 1 interface allows the ion channel to close and thereby provides a simple explanation to the long-standing question of how agonist binding is decoupled from ion channel gating upon receptor desensitization.

    Related Citations: 
    • Probing the ligand binding domain of the GluR2 receptor by proteolysis and deletion mutagenesis defines domain boundaries and yields a crystallizable construct
      Chen, G.Q., Sun, Y., Jin, R., Gouaux, E.
      (1998) Protein Sci 7: 2623
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUTAMATE RECEPTOR SUBUNIT 2A, B259Rattus norvegicusMutation(s): 0 
Gene Names: Gria2
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU
Download Ideal Coordinates CCD File 
A, B
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GGLEC50:  35000   nM  BindingDB
GGLEC50:  100000   nM  BindingDB
GGLEC50:  14000   nM  BindingDB
GGLEC50:  51000   nM  BindingDB
GGLEC50:  67000   nM  BindingDB
GGLEC50:  140000   nM  BindingDB
GGLKi:  89   nM  BindingDB
GGLEC50:  190000   nM  BindingDB
GGLEC50:  3660   nM  BindingDB
GGLKi:  10000   nM  BindingDB
GGLKi:  280   nM  BindingDB
GGLEC50:  6200   nM  BindingDB
GGLKi:  282   nM  BindingDB
GGLEC50:  3400   nM  BindingDB
GGLEC50:  52000   nM  BindingDB
GGLEC50:  140000   nM  BindingDB
GGLKi:  62   nM  BindingDB
GGLKi:  169   nM  BindingDB
GGLEC50:  6400   nM  BindingDB
GGLEC50:  35000   nM  BindingDB
GGLKi:  940   nM  BindingDB
GGLEC50:  1300   nM  BindingDB
GGLKi:  500   nM  BindingDB
GGLEC50:  12500   nM  BindingDB
GGLEC50:  19600   nM  BindingDB
GGLEC50:  20000   nM  BindingDB
GGLKi:  7400   nM  BindingDB
GGLEC50:  21200   nM  BindingDB
GGLEC50:  14700   nM  BindingDB
GGLEC50:  2190   nM  BindingDB
GGLEC50:  17000   nM  BindingDB
GGLKi:  354   nM  BindingDB
GGLKi:  336   nM  BindingDB
GGLKi:  249   nM  BindingDB
GGLKi:  254   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.002α = 90
b = 93.142β = 90
c = 138.244γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-16
    Changes: Refinement description, Source and taxonomy