3FAT

X-ray structure of iGluR4 flip ligand-binding core (S1S2) in complex with (S)-AMPA at 1.90A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism of agonist recognition by the ligand-binding core of the ionotropic glutamate receptor 4

Kasper, C.Frydenvang, K.Naur, P.Gajhede, M.Pickering, D.S.Kastrup, J.S.

(2008) FEBS Lett 582: 4089-4094

  • DOI: 10.1016/j.febslet.2008.11.005
  • Primary Citation of Related Structures:  
    3FAS, 3FAT

  • PubMed Abstract: 
  • The alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) class of ionotropic glutamate receptors comprises four different subunits: iGluR1/iGluR2 and iGluR3/iGluR4 forming two subgroups. Three-dimensional structures have been reported only of the ligand-binding core of iGluR2 ...

    The alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) class of ionotropic glutamate receptors comprises four different subunits: iGluR1/iGluR2 and iGluR3/iGluR4 forming two subgroups. Three-dimensional structures have been reported only of the ligand-binding core of iGluR2. Here, we present two X-ray structures of a soluble construct of the R/G unedited flip splice variant of the ligand-binding core of iGluR4 (iGluR4(i)(R)-S1S2) in complex with glutamate or AMPA. Subtle, but important differences are found in the ligand-binding cavity between the two AMPA receptor subgroups at position 724 (Tyr in iGluR1/iGluR2 and Phe in iGluR3/iGluR4), which in iGluR4 may lead to displacement of a water molecule and hence points to the possibility to make subgroup specific ligands.


    Organizational Affiliation

    Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 4A, B, C260Rattus norvegicusMutation(s): 0 
Gene Names: Gria4
Find proteins for P19493 (Rattus norvegicus)
Explore P19493 
Go to UniProtKB:  P19493
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMQ
Query on AMQ

Download Ideal Coordinates CCD File 
D [auth A], K [auth B], T [auth C](S)-ALPHA-AMINO-3-HYDROXY-5-METHYL-4-ISOXAZOLEPROPIONIC ACID
C7 H10 N2 O4
UUDAMDVQRQNNHZ-YFKPBYRVSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], U [auth C], V [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A] , M [auth B] , N [auth B] , O [auth B] , P [auth B] , W [auth C] , X [auth C] , Y [auth C] , 
I [auth A],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  W [auth C],  X [auth C],  Y [auth C],  Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
AA [auth C], BA [auth C], J [auth A], Q [auth B], R [auth B], S [auth B]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AMQKd :  22.799999237060547   nM  PDBBind
AMQKd:  22.799999237060547   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.175α = 90
b = 169.531β = 120.58
c = 73.883γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-08-09
    Changes: Data collection, Refinement description, Source and taxonomy