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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLUR4 LIGAND-BINDING DOMAIN IN COMPLEX WITH GLUTAMATE
 
Authors :  A. Gill, D. R. Madden
Date :  29 Sep 08  (Deposition) - 19 May 09  (Release) - 19 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glur4, Ampa Receptor, Ligand-Gated Ion Channel, Ligand- Binding Domain, Kainate, Alternative Splicing, Cell Junction, Cell Membrane, Glycoprotein, Ion Transport, Ionic Channel, Lipoprotein, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Gill, A. Birdsey-Benson, B. L. Jones, L. P. Henderson, D. R. Madden
Correlating Ampa Receptor Activation And Cleft Closure Across Subunits: Crystal Structures Of The Glur4 Ligand-Binding Domain In Complex With Full And Partial Agonists
Biochemistry V. 47 13831 2008
PubMed-ID: 19102704  |  Reference-DOI: 10.1021/BI8013196
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR 4,GLUTAMATE RECEPTOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET16-B
    Expression System StrainXJB(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentLIGAND BINDING DOMAIN (UNP RESIDUES 416-528 AND 654-958)
    GeneGLUR4,GLUTAMATE RECEPTOR
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    StrainSPRAGUE-DAWLEY

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GLU2Mod. Amino AcidGLUTAMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:57 , PRO B:85 , LEU B:86 , THR B:87 , ARG B:92 , GLY B:137 , SER B:138 , THR B:139 , GLU B:189 , HOH B:261 , HOH B:265 , HOH B:268BINDING SITE FOR RESIDUE GLU B 258
2AC2SOFTWARETYR A:57 , PRO A:85 , LEU A:86 , THR A:87 , ARG A:92 , GLY A:137 , SER A:138 , THR A:139 , GLU A:189 , TYR A:216 , HOH A:261 , HOH A:274 , HOH A:322BINDING SITE FOR RESIDUE GLU A 258

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:202 -A:257
2B:202 -B:257

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser A:10 -Pro A:11
2Glu A:162 -Pro A:163
3Lys A:200 -Pro A:201
4Ser B:10 -Pro B:11
5Glu B:162 -Pro B:163
6Lys B:200 -Pro B:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EPE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EPE)

(-) Exons   (0, 0)

(no "Exon" information available for 3EPE)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:258
 aligned with GRIA4_RAT | P19493 from UniProtKB/Swiss-Prot  Length:902

    Alignment length:381
                                   425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795 
            GRIA4_RAT   416 TVVVTTIMESPYVMYKKNHEMFEGNDKYEGYCVDLASEIAKHIGIKYKIAIVPDGKYGARDADTKIWNGMVGELVYGKAEIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEPEDGKEGPSDQPPNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMRSAEPSVFTRTTAEGVARVRKSKGKFAFLLESTMNEYTEQRKPCDTMKVGGNLDSKGYGVATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGECG 796
               SCOP domains d3epea_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3epeA01 A:1-105,A:215-254 Periplasmic binding protein-like II                                            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3epeA01 A:1-105,A:215-254               ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......ee..hhhhhhhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee..---------------------------------------------------------------------------------------------------------------------------....hhhhhhh....eeee...hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3epe A   1 TVVVTTIMESPYVMYKKNHEMFEGNDKYEGYCVDLASEIAKHIGIKYKIAIVPDGKYGARDADTKIWNGMVGELVYGKAEIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKG---------------------------------------------------------------------------------------------------------------------------TPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMRSAEPSVFTRTTAEGVARVRKSKGKFAFLLESTMNEYTEQRKPCDTMKVGGNLDSKGYGVATPKGSSLRTPVNLAVLKLSEAGVLDKLKNKWWYDKGECE 258
                                    10        20        30        40        50        60        70        80        90       100       110   |     -         -         -         -         -         -         -         -         -         -         -         -       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257 
                                                                                                                                           114                                                                                                                         115                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:258
 aligned with GRIA4_RAT | P19493 from UniProtKB/Swiss-Prot  Length:902

    Alignment length:381
                                   425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795 
            GRIA4_RAT   416 TVVVTTIMESPYVMYKKNHEMFEGNDKYEGYCVDLASEIAKHIGIKYKIAIVPDGKYGARDADTKIWNGMVGELVYGKAEIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEPEDGKEGPSDQPPNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMRSAEPSVFTRTTAEGVARVRKSKGKFAFLLESTMNEYTEQRKPCDTMKVGGNLDSKGYGVATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGECG 796
               SCOP domains d3epeb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3epeB01 B:1-105,B:215-254 Periplasmic binding protein-like II                                            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3epeB01 B:1-105,B:215-254               ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......ee..hhhhhhhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee..---------------------------------------------------------------------------------------------------------------------------....hhhhhhh....eeeee..hhhhhhhhhh.hhhhhhhhhhhhhh....ee.hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3epe B   1 TVVVTTIMESPYVMYKKNHEMFEGNDKYEGYCVDLASEIAKHIGIKYKIAIVPDGKYGARDADTKIWNGMVGELVYGKAEIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKG---------------------------------------------------------------------------------------------------------------------------TPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMRSAEPSVFTRTTAEGVARVRKSKGKFAFLLESTMNEYTEQRKPCDTMKVGGNLDSKGYGVATPKGSSLRTPVNLAVLKLSEAGVLDKLKNKWWYDKGECE 258
                                    10        20        30        40        50        60        70        80        90       100       110   |     -         -         -         -         -         -         -         -         -         -         -         -       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257 
                                                                                                                                           114                                                                                                                         115                                                                                                                                               

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EPE)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GRIA4_RAT | P19493)
molecular function
    GO:0004971    AMPA glutamate receptor activity    An ionotropic glutamate receptor activity that exhibits fast gating by glutamate and acts by opening a cation channel permeable to sodium, potassium, and, in the absence of a GluR2 subunit, calcium.
    GO:0005234    extracellular-glutamate-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when extracellular glutamate has been bound by the channel complex or one of its constituent parts.
    GO:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
    GO:0004970    ionotropic glutamate receptor activity    Catalysis of the transmembrane transfer of an ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0035235    ionotropic glutamate receptor signaling pathway    A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0050804    modulation of chemical synaptic transmission    Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission.
    GO:0051968    positive regulation of synaptic transmission, glutamatergic    Any process that activates, maintains or increases the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate.
    GO:0050803    regulation of synapse structure or activity    Any process that modulates the physical form or the activity of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
    GO:0060992    response to fungicide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fungicide stimulus. Fungicides are chemicals used to kill fungi.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0032281    AMPA glutamate receptor complex    An assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex. The AMPA receptors mediate fast synaptic transmission in the CNS and are composed of subunits GluR1-4, products from separate genes. These subunits have an extracellular N-terminus and an intracellular C-terminus.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0008328    ionotropic glutamate receptor complex    A multimeric assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand-gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex.
    GO:0032983    kainate selective glutamate receptor complex    An assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex. Kainate receptors are multimeric assemblies of GluK1-3 (also called GluR5-7), GluK4 (KA1) and GluK5 (KA2) subunits.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    GO:0043195    terminal bouton    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        GRIA4_RAT | P194933en3 3fas 3fat 3kei 3kfm 4gpa 5fwx

(-) Related Entries Specified in the PDB File

3en3 CRYSTAL STRUCTURE OF THE GLUR4 LIGAND-BINDING DOMAIN IN COMPLEX WITH KAINATE