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(-) Description

Title :  FLUOROWILLARDIINE BOUND TO THE LIGAND BINDING DOMAIN OF GLUA3
 
Authors :  A. H. Ahmed, R. E. Oswald
Date :  03 May 11  (Deposition) - 18 May 11  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.84
Chains :  Asym. Unit :  B
Biol. Unit 1:  B  (2x)
Keywords :  Glutamate Receptor, Glur3, Ampa Receptor, S1S2, Neurotransmitter Receptor, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Poon, A. H. Ahmed, L. M. Nowak, R. E. Oswald
Mechanisms Of Modal Activation Of Glua3 Receptors.
Mol. Pharmacol. V. 80 49 2011
PubMed-ID: 21464198  |  Reference-DOI: 10.1124/MOL.111.071688

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR 3
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-22B(+)
    Expression System StrainORIGAMI B(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSEE REMARK 999
    GeneGLUA3, GLUR3, GRIA3
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymGLUA3, GLUR-3, AMPA-SELECTIVE GLUTAMATE RECEPTOR 3, GLUR-C, GLUR-K3, GLUTAMATE RECEPTOR IONOTROPIC, AMPA 3

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit B
Biological Unit 1 (2x)B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1FWD1Ligand/Ion2-AMINO-3-(5-FLUORO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1FWD2Ligand/Ion2-AMINO-3-(5-FLUORO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:61 , PRO B:89 , LEU B:90 , THR B:91 , ARG B:96 , LEU B:138 , GLY B:141 , SER B:142 , THR B:143 , LEU B:192 , GLU B:193 , MET B:196 , HOH B:264BINDING SITE FOR RESIDUE FWD B 401
2AC2SOFTWAREHIS B:23 , GLU B:24BINDING SITE FOR RESIDUE ZN B 1

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:206 -B:261

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser B:14 -Pro B:15
2Glu B:166 -Pro B:167
3Lys B:204 -Pro B:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RT6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RT6)

(-) Exons   (0, 0)

(no "Exon" information available for 3RT6)

(-) Sequences/Alignments

Asymmetric 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 B from PDB  Type:PROTEIN  Length:258
 aligned with GRIA3_RAT | P19492 from UniProtKB/Swiss-Prot  Length:888

    Alignment length:383
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796   
            GRIA3_RAT   417 RTIVVTTILESPYVMYKKNHEQLEGNERYEGYCVDLAYEIAKHVRIKYKLSIVGDGKYGARDPETKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHLEDNNEEPRDPQSPPDPPNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWSYMKSAEPSVFTKTTADGVARVRKSKGKFAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGVATPKGSALGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 799
               SCOP domains d3rt6b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------Lig_chan-Glu_bd-3rt6B02 B:15-80                                   -------------------------------------------------------------------------------------------------------------------------------------------------------------------Lig_chan-3rt6B01 B:119-261                                                                                                                      Pfam domains
         Sec.struct. author ..eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee..-----------------------------------------------------------------------------------------------------------------------------....hhhhhhh....eeee...hhhhhhhhhh.hhhhhhhhhhhhh........hhhhhhhhhhh....eeeeeehhhhhhhh......eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rt6 B   4 RTIVVTTILESPYVMYKKNHEQLEGNERYEGYCVDLAYEIAKHVRIKYKLSIVGDGKYGARDPETKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKG-----------------------------------------------------------------------------------------------------------------------------TPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWSYMKSAEPSVFTKTTADGVARVRKSKGKFAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGVATPKGSALGTPVNLAVLKLSEQGILDKLKNKWWYDKGEC 261
                                    13        23        33        43        53        63        73        83        93       103       113    |    -         -         -         -         -         -         -         -         -         -         -         -         -|      128       138       148       158       168       178       188       198       208       218       228       238       248       258   
                                                                                                                                            118                                                                                                                           119                                                                                                                                              

   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, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RT6)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)
Chain B   (GRIA3_RAT | P19492)
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:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    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: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:0001919    regulation of receptor recycling    Any process that modulates the frequency, rate, or extent of receptor recycling.
    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:0010226    response to lithium ion    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 lithium (Li+) ion stimulus.
    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:0032279    asymmetric synapse    A type of synapse occurring between an axon and a dendritic spine or dendritic shaft. Asymmetric synapses, the most abundant synapse type in the central nervous system, involve axons that contain predominantly spherical vesicles and contain a thickened postsynaptic density. Most or all synapses of this type are excitatory.
    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: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:0043198    dendritic shaft    Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    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: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:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    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:0043083    synaptic cleft    The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released.
    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)

UniProtKB/Swiss-Prot
        GRIA3_RAT | P194923dln 3dp4 3lsw 3lsx 3m3f 3m3k 3o21 3p3w 3rt8 4f1y 4f22 4f29 4f2o 4f2q 4f31 4f39 4f3b 4f3g 5fwy 5ide 5idf

(-) Related Entries Specified in the PDB File

3rt8 3rtf 3rtw