2I3V

Measurement of conformational changes accompanying desensitization in an ionotropic glutamate receptor: Structure of G725C mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

wwPDB Validation 3D Report Full Report


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
  • Structures With Same Primary Citation

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2A, B, C, D259Rattus norvegicusMutation(s): 0 
Gene Names: Gria2Glur2
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

Download CCD File 
A, B, C, D
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GGLEC50:  35000   nM  BindingDB
GGLEC50:  12500   nM  BindingDB
GGLKi:  940   nM  BindingDB
GGLEC50:  2190   nM  BindingDB
GGLEC50:  52000   nM  BindingDB
GGLKi:  7400   nM  BindingDB
GGLEC50:  3660   nM  BindingDB
GGLKi:  500   nM  BindingDB
GGLEC50:  14700   nM  BindingDB
GGLEC50:  67000   nM  BindingDB
GGLKi:  354   nM  BindingDB
GGLKi:  336   nM  BindingDB
GGLEC50:  100000   nM  BindingDB
GGLKi:  254   nM  BindingDB
GGLKi:  249   nM  BindingDB
GGLEC50:  14000   nM  BindingDB
GGLEC50:  140000   nM  BindingDB
GGLEC50:  3400   nM  BindingDB
GGLEC50:  51000   nM  BindingDB
GGLEC50:  140000   nM  BindingDB
GGLEC50:  190000   nM  BindingDB
GGLEC50:  35000   nM  BindingDB
GGLKi:  10000   nM  BindingDB
GGLEC50:  17000   nM  BindingDB
GGLEC50:  19600   nM  BindingDB
GGLKi:  89   nM  BindingDB
GGLEC50:  20000   nM  BindingDB
GGLKi:  280   nM  BindingDB
GGLKi:  282   nM  BindingDB
GGLEC50:  1300   nM  BindingDB
GGLEC50:  21200   nM  BindingDB
GGLEC50:  6200   nM  BindingDB
GGLEC50:  6400   nM  BindingDB
GGLKi:  169   nM  BindingDB
GLUKi :  282   nM  PDBBind
GGLKi:  62   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.191α = 90
b = 106.291β = 90
c = 192.817γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



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