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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLUR5 LIGAND BINDING CORE DIMER IN COMPLEX WITH UBP318 AT 1.80 ANGSTROMS RESOLUTION
 
Authors :  G. M. Alushin, D. E. Jane, M. L. Mayer
Date :  30 Jul 07  (Deposition) - 05 Aug 08  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Membrane Protein, Cell Junction, Glycoprotein, Ion Transport, Ionic Channel, Phosphorylation, Postsynaptic Cell Membrane, Receptor, Rna Editing, Synapse, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. M. Alushin, D. Jane, M. L. Mayer
Binding Site And Ligand Flexibility Revealed By High Resolution Crystal Structures Of Gluk1 Competitive Antagonists.
Neuropharmacology V. 60 126 2011
PubMed-ID: 20558186  |  Reference-DOI: 10.1016/J.NEUROPHARM.2010.06.002

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B (MODIFIED)
    Expression System StrainORIGAMI B (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGRIK1, GLUR5
    MutationYES
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymGLUTAMATE RECEPTOR 5, GLUR-5, GLUR5

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)A 
Biological Unit 2 (2x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2CL2Ligand/IonCHLORIDE ION
3UBF2Ligand/Ion3-({3-[(2S)-2-AMINO-2-CARBOXYETHYL]-5-BROMO-2,6-DIOXO-3,6-DIHYDROPYRIMIDIN-1(2H)-YL}METHYL)THIOPHENE-2-CARBOXYLIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2CL-1Ligand/IonCHLORIDE ION
3UBF2Ligand/Ion3-({3-[(2S)-2-AMINO-2-CARBOXYETHYL]-5-BROMO-2,6-DIOXO-3,6-DIHYDROPYRIMIDIN-1(2H)-YL}METHYL)THIOPHENE-2-CARBOXYLIC ACID
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2CL-1Ligand/IonCHLORIDE ION
3UBF2Ligand/Ion3-({3-[(2S)-2-AMINO-2-CARBOXYETHYL]-5-BROMO-2,6-DIOXO-3,6-DIHYDROPYRIMIDIN-1(2H)-YL}METHYL)THIOPHENE-2-CARBOXYLIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:103 , ARG A:227 , HOH A:615BINDING SITE FOR RESIDUE CL A 501
2AC2SOFTWARELYS B:103 , ARG B:227 , HOH B:610BINDING SITE FOR RESIDUE CL B 502
3AC3SOFTWAREARG B:20 , LYS B:21 , SER B:22 , ASP B:23 , HOH B:738 , HOH B:803BINDING SITE FOR RESIDUE 1PE B 601
4AC4SOFTWAREARG A:20 , LYS A:21 , SER A:22 , ASP A:23 , HOH A:631 , HOH A:680BINDING SITE FOR RESIDUE 1PE A 602
5AC5SOFTWAREGLU A:13 , TYR A:61 , PRO A:88 , LEU A:89 , THR A:90 , ARG A:95 , SER A:141 , THR A:142 , GLU A:190 , TYR A:216 , HOH A:624 , HOH A:697 , HOH A:701 , HOH A:716 , HOH A:745 , HOH A:765 , HOH A:813BINDING SITE FOR RESIDUE UBF A 603
6AC6SOFTWAREGLU B:13 , TYR B:61 , PRO B:88 , LEU B:89 , THR B:90 , ARG B:95 , SER B:141 , THR B:142 , GLU B:190 , TYR B:216 , HOH B:623 , HOH B:656 , HOH B:666 , HOH B:671 , HOH B:710 , HOH B:805BINDING SITE FOR RESIDUE UBF B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QS2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:14 -Pro A:15
2Glu B:14 -Pro B:15

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QS2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QS2)

(-) Exons   (0, 0)

(no "Exon" information available for 2QS2)

(-) 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 A from PDB  Type:PROTEIN  Length:251
 aligned with GRIK1_RAT | P22756 from UniProtKB/Swiss-Prot  Length:949

    Alignment length:371
                                   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       806       816 
            GRIK1_RAT   447 RTLIVTTILEEPYVMYRKSDKPLYGNDRFEAYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKPNGTNPGVFSFLNPLSPDIWMYVLLACLGVSCVLFVIARFTPYEWYNPHPCNPDSDVVENNFTLLNSFWFGVGALMQQGSELMPKALSTRIVGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGN 817
               SCOP domains d2qs2a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2qs2A01 A:4-108,A:214-254 Periplasmic binding protein-like II                                            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2qs2A01 A:4-108,A:214-254                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee.--..----------------------------------------------------------------------------------------------------------------------...hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.eeeeeehhhhhhhhh....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qs2 A   4 RTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRK--GT----------------------------------------------------------------------------------------------------------------------PIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGN 254
                                    13        23        33        43        53        63        73        83        93       103       113  |  ||  -         -         -         -         -         -         -         -         -         -         -         -     | 123       133       143       153       163       173       183       193       203       213       223       233       243       253 
                                                                                                                                          116  ||                                                                                                                    119                                                                                                                                       
                                                                                                                                             117|                                                                                                                                                                                                                                                              
                                                                                                                                              118                                                                                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:251
 aligned with GRIK1_RAT | P22756 from UniProtKB/Swiss-Prot  Length:949

    Alignment length:371
                                   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       806       816 
            GRIK1_RAT   447 RTLIVTTILEEPYVMYRKSDKPLYGNDRFEAYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKPNGTNPGVFSFLNPLSPDIWMYVLLACLGVSCVLFVIARFTPYEWYNPHPCNPDSDVVENNFTLLNSFWFGVGALMQQGSELMPKALSTRIVGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGN 817
               SCOP domains d2qs2b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2qs2B01 B:4-108,B:214-254 Periplasmic binding protein-like II                                            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2qs2B01 B:4-108,B:214-254                 CATH domains
           Pfam domains (1) -----------Lig_chan-Glu_bd-2qs2B03 B:15-79                                  ---------------------------------------------------------------------------------------------------------------------------------------------------------------Lig_chan-2qs2B01 B:119-254                                                                                                               Pfam domains (1)
           Pfam domains (2) -----------Lig_chan-Glu_bd-2qs2B04 B:15-79                                  ---------------------------------------------------------------------------------------------------------------------------------------------------------------Lig_chan-2qs2B02 B:119-254                                                                                                               Pfam domains (2)
         Sec.struct. author ..eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee.--..----------------------------------------------------------------------------------------------------------------------...hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.eeeeeehhhhhhhhh....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qs2 B   4 RTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRK--GT----------------------------------------------------------------------------------------------------------------------PIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGN 254
                                    13        23        33        43        53        63        73        83        93       103       113  |  ||  -         -         -         -         -         -         -         -         -         -         -         -     | 123       133       143       153       163       173       183       193       203       213       223       233       243       253 
                                                                                                                                          116  ||                                                                                                                    119                                                                                                                                       
                                                                                                                                             117|                                                                                                                                                                                                                                                              
                                                                                                                                              118                                                                                                                                                                                                                                                              

   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 Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (33, 33)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GRIK1_RAT | P22756)
molecular function
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    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:0016595    glutamate binding    Interacting selectively and non-covalently with glutamate, the anion of 2-aminopentanedioic acid.
    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:0015277    kainate selective glutamate receptor activity    An ionotropic glutamate receptor activity that exhibits fast gating by glutamate, acts by opening a cation channel permeable to sodium and potassium, and for which kainate is an agonist.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0022843    voltage-gated cation channel activity    Enables the transmembrane transfer of a cation by a voltage-gated channel. A cation is a positively charged ion. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
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:0032229    negative regulation of synaptic transmission, GABAergic    Any process that stops, prevents, or reduces the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA).
    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:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0032230    positive regulation of synaptic transmission, GABAergic    Any process that activates, maintains or increases the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA).
    GO:0034765    regulation of ion transmembrane transport    Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
    GO:0048172    regulation of short-term neuronal synaptic plasticity    A process that modulates short-term neuronal synaptic plasticity, the ability of neuronal synapses to change in the short-term as circumstances require. Short-term neuronal synaptic plasticity generally involves increasing or decreasing synaptic sensitivity.
    GO:0048167    regulation of synaptic plasticity    A process that modulates synaptic plasticity, the ability of synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
    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: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: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: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:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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
        GRIK1_RAT | P227561txf 1vso 1ycj 2f34 2f35 2f36 2ojt 2pbw 2qs1 2qs3 2qs4 2wky 3c31 3c32 3c33 3c34 3c35 3c36 3gba 3gbb 3s2v 4dld 4e0x 4qf9 4ymb 5m2v 5mfq 5mfv 5mfw

(-) Related Entries Specified in the PDB File

1txf CRYSTAL STRUCTURE OF THE GLUR5 LIGAND BINDING CORE DIMER IN COMPLEX WITH GLUTAMATE AT 2.1 ANGSTROMS RESOLUTION
2f34 CRYSTAL STRUCTURE OF THE GLUR5 LIGAND BINDING CORE DIMER IN COMPLEX WITH UBP310 AT 1.74 ANGSTROMS RESOLUTION
2f35 CRYSTAL STRUCTURE OF THE GLUR5 LIGAND BINDING CORE DIMER IN COMPLEX WITH UBP302 AT 1.87 ANGSTROMS RESOLUTION
2f36 CRYSTAL STRUCTURE OF THE GLUR5 LIGAND BINDING CORE DIMER IN COMPLEX WITH GLUTAMATE AT 2.1 ANGSTROMS RESOLUTION
2qs1
2qs3
2qs4