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(-) Description

Title :  CRYSTAL STRUCTURE OF THE KAINATE RECEPTOR GLUK3 LIGAND BINDING DOMAIN IN COMPLEX WITH (S)-GLUTAMATE
 
Authors :  R. Venskutonyte, K. Frydenvang, M. Gajhede, J. S. Kastrup
Date :  01 Jun 11  (Deposition) - 28 Sep 11  (Release) - 02 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Agonist, Ionotropic Glutamate Receptor, Glutamate, Membrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Venskutonyte, K. Frydenvang, M. Gajhede, L. Bunch, D. S. Pickering J. S. Kastrup
Binding Site And Interlobe Interactions Of The Ionotropic Glutamate Receptor Gluk3 Ligand Binding Domain Revealed By High Resolution Crystal Structure In Complex With (S)-Glutamate.
J. Struct. Biol. V. 176 307 2011
PubMed-ID: 21907808  |  Reference-DOI: 10.1016/J.JSB.2011.08.014

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPOPINJ
    Expression System StrainORIGAMI2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGRIK3
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2GLU2Mod. Amino AcidGLUTAMIC ACID
3GOL1Ligand/IonGLYCEROL
4NA3Ligand/IonSODIUM ION
5PO43Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:63 , PRO A:90 , LEU A:91 , THR A:92 , ARG A:97 , GLY A:142 , ALA A:143 , THR A:144 , GLU A:191 , HOH A:277 , HOH A:296 , HOH A:346 , HOH A:384BINDING SITE FOR RESIDUE GLU A 259
02AC2SOFTWARELYS A:99 , HOH A:355 , HOH A:508 , HOH A:759 , THR B:109 , HOH B:309 , HOH B:558BINDING SITE FOR RESIDUE GOL A 260
03AC3SOFTWAREGLN A:239 , ASP A:242 , LEU A:244 , HIS A:245BINDING SITE FOR RESIDUE CL A 261
04AC4SOFTWAREARG A:33 , LEU A:57BINDING SITE FOR RESIDUE CL A 262
05AC5SOFTWARELYS A:62 , LYS A:140 , HOH A:405 , HOH A:751BINDING SITE FOR RESIDUE PO4 A 263
06AC6SOFTWARELYS A:250 , LYS B:250BINDING SITE FOR RESIDUE PO4 A 264
07AC7SOFTWARESER A:24 , ARG A:26 , HOH A:348 , HOH A:362 , HOH A:369 , HOH B:546BINDING SITE FOR RESIDUE NA A 265
08AC8SOFTWARETYR B:63 , PRO B:90 , LEU B:91 , THR B:92 , ARG B:97 , GLY B:142 , ALA B:143 , THR B:144 , GLU B:191 , HOH B:269 , HOH B:276 , HOH B:330 , HOH B:371BINDING SITE FOR RESIDUE GLU B 259
09AC9SOFTWAREGLN B:239 , ASP B:242 , LEU B:244 , HIS B:245BINDING SITE FOR RESIDUE CL B 260
10BC1SOFTWAREARG B:33 , LEU B:57 , HOH B:809BINDING SITE FOR RESIDUE CL B 261
11BC2SOFTWARELYS B:62 , LYS B:140 , HOH B:754BINDING SITE FOR RESIDUE PO4 B 262
12BC3SOFTWARESER B:24 , ARG B:26 , HOH B:304 , HOH B:359 , HOH B:405 , HOH B:480 , HOH B:484BINDING SITE FOR RESIDUE NA B 263
13BC4SOFTWAREASN A:5 , SER A:52 , HOH A:266 , HOH A:442 , ASN B:5 , SER B:52 , HOH B:265 , HOH B:668BINDING SITE FOR RESIDUE NA B 264

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:203 -A:257
2B:203 -B:257

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:16 -Pro A:17
2Glu B:16 -Pro B:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S9E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S9E)

(-) Exons   (0, 0)

(no "Exon" information available for 3S9E)

(-) 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:254
 aligned with GRIK3_RAT | P42264 from UniProtKB/Swiss-Prot  Length:919

    Alignment length:384
                                   433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803    
            GRIK3_RAT   424 GPNVTDSLTNRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLGVSILYRKPNGTNPSVFSFLNPLSPDIWMYVLLAYLGVSCVLFVIARFSPYEWYDAHPCNPGSEVVENNFTLLNSFWFGMGSLMQQGSELMPKALSTRIIGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFEKMWAFMSSKPSALVKNNEEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRGSGCPE 807
               SCOP domains d       3s9ea_ A: automated matches                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .-------....eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....eeeeeee.hhhhhh.eee....eee.eeeeee.--..----------------------------------------------------------------------------------------------------------------------...hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhh........hhhhhhhhhhhh.eeeeeehhhhhhhhhhh..eeee......eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh---... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3s9e A   3 G-------TNRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLGVSILYRK--GT----------------------------------------------------------------------------------------------------------------------PIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFEKMWAFMSSKPSALVKNNEEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWR---CPE 259
                            |       |5        15        25        35        45        55        65        75        85        95       105       115  |  ||  -         -         -         -         -         -         -         -         -         -         -         -     | 125       135       145       155       165       175       185       195       205       215       225       235       245       | - |  
                            |       4                                                                                                               118  ||                                                                                                                    121                                                                                                                                 253 257  
                            3                                                                                                                          119|                                                                                                                                                                                                                                                                 
                                                                                                                                                        120                                                                                                                                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:254
 aligned with GRIK3_RAT | P42264 from UniProtKB/Swiss-Prot  Length:919

    Alignment length:384
                                   433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803    
            GRIK3_RAT   424 GPNVTDSLTNRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLGVSILYRKPNGTNPSVFSFLNPLSPDIWMYVLLAYLGVSCVLFVIARFSPYEWYDAHPCNPGSEVVENNFTLLNSFWFGMGSLMQQGSELMPKALSTRIIGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFEKMWAFMSSKPSALVKNNEEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRGSGCPE 807
               SCOP domains d       3s9eb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .-------....eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....eeeeeee.hhhhhh.eee....eee.eeeeee.--..----------------------------------------------------------------------------------------------------------------------...hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhh.hhhhh..hhhhhhhhhhhh.eeeeeehhhhhhhhhhh..eeee......eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh---... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3s9e B   3 G-------TNRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLGVSILYRK--GT----------------------------------------------------------------------------------------------------------------------PIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFEKMWAFMSSKPSALVKNNEEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWR---CPE 259
                            |       |5        15        25        35        45        55        65        75        85        95       105       115  |  ||  -         -         -         -         -         -         -         -         -         -         -         -     | 125       135       145       155       165       175       185       195       205       215       225       235       245       | - |  
                            3       4                                                                                                               118  ||                                                                                                                    121                                                                                                                                 253 257  
                                                                                                                                                       119|                                                                                                                                                                                                                                                                 
                                                                                                                                                        120                                                                                                                                                                                                                                                                 

   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  (0, 0)

(no "CATH Domain" information available for 3S9E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S9E)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GRIK3_RAT | P42264)
molecular function
    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:0008066    glutamate receptor activity    Combining with glutamate and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    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: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:0051967    negative regulation of synaptic transmission, glutamatergic    Any process that stops, prevents, or reduces 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:0042391    regulation of membrane potential    Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    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:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    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:0032839    dendrite cytoplasm    All of the contents of a dendrite, excluding the surrounding plasma membrane.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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: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)

UniProtKB/Swiss-Prot
        GRIK3_RAT | P422643olz 3u92 3u93 3u94 4e0w 4g8n 4igr 4mh5 4nwc 4nwd

(-) Related Entries Specified in the PDB File

4mh5 SAME CRYSTAL STRUCTURE IN A DIFFERENT SPACE GROUP