3DP6

Crystal structure of the binding domain of the AMPA subunit GluR2 bound to glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the S1S2 glutamate binding domain of GLuR3.

Ahmed, A.H.Wang, Q.Sondermann, H.Oswald, R.E.

(2008) Proteins 75: 628-637

  • DOI: 10.1002/prot.22274
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Glutamate receptors are the most prevalent excitatory neurotransmitter receptors in the vertebrate central nervous system. Determining the structural differences between the binding sites of different subtypes is crucial to our understanding of neuro ...

    Glutamate receptors are the most prevalent excitatory neurotransmitter receptors in the vertebrate central nervous system. Determining the structural differences between the binding sites of different subtypes is crucial to our understanding of neuronal circuits and to the development of subtype specific drugs. The structures of the binding domain (S1S2) of the GluR3 (flip) AMPA receptor subunit bound to glutamate and AMPA and the GluR2 (flop) subunit bound to glutamate were determined by X-ray crystallography to 1.9, 2.1, and 1.55 A, respectively. Overall, the structure of GluR3 (flip) S1S2 is very similar to GluR2 (flop) S1S2 (backbone RMSD of 0.30 +/- 0.05 for glutamate-bound and 0.26 +/- 0.01 for AMPA-bound). The differences in the flip and flop isoforms are subtle and largely arise from one hydrogen bond across the dimer interface and associated water molecules. Comparison of the binding affinity for various agonists and partial agonists suggest that the S1S2 domains of GluR2 and GluR3 show only small differences in affinity, unlike what is found for the intact receptors (with the exception of one ligand, Cl-HIBO, which has a 10-fold difference in affinity for GluR2 vs. GluR3).


    Organizational Affiliation

    Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
A, B, C
279Rattus norvegicusMutation(s): 0 
Gene Names: Gria2Glur2
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.84α = 90
b = 163.184β = 90
c = 47.324γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-02
    Changes: Source and taxonomy