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(-) Description

Title :  STRUCTURE OF THE LIGAND-BINDING CORE OF THE IONOTROPIC GLUTAMATE RECEPTOR-LIKE GLURDELTA2 IN COMPLEX WITH D-SERINE
 
Authors :  P. Naur, B. Vestergaard, M. Gajhede, J. S. Kastrup
Date :  22 Jun 07  (Deposition) - 07 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym./Biol. Unit :  A
Keywords :  Postsynaptic Membrane, Ionotropic Glutamate Receptors, Transmembrane, Membrane Protein, Ligand-Binding Core, Glycoprotein, Ionic Channel, Ion Transport, Membrane, Receptor, D-Serine, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Naur, K. B. Hansen, A. S. Kristensen, S. M. Dravid, D. S. Pickering, L. Olsen, B. Vestergaard, J. Egebjerg, M. Gajhede, S. F. Traynelis, J. S. Kastrup
Ionotropic Glutamate-Like Receptor {Delta}2 Binds D-Serine And Glycine.
Proc. Nat. Acad. Sci. Usa V. 104 14116 2007
PubMed-ID: 17715062  |  Reference-DOI: 10.1073/PNAS.0703718104

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR DELTA-2 SUBUNIT
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainORIGAMI 2
    Expression System Taxid562
    FragmentLIGAND-BINDING CORE, RESIDUES 440-551,664-813
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymGLURDELTA2, GLUR DELTA-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2DSN1Ligand/IonD-SERINE
3NA1Ligand/IonSODIUM ION
4SCN2Ligand/IonTHIOCYANATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:58 , ALA A:85 , THR A:87 , ARG A:92 , TYR A:105 , SER A:137 , ALA A:138 , VAL A:139 , TRP A:193 , ASP A:194BINDING SITE FOR RESIDUE DSN A1262
2AC2SOFTWAREGLU A:93 , VAL A:96 , ASP A:97 , HOH A:2054 , HOH A:2114BINDING SITE FOR RESIDUE NA A1263
3AC3SOFTWARELEU A:11 , VAL A:52 , HOH A:2038BINDING SITE FOR RESIDUE CL A1264
4AC4SOFTWAREGLY A:59 , THR A:89 , ARG A:92 , GLN A:141BINDING SITE FOR RESIDUE SCN A1265
5AC5SOFTWARETYR A:105 , ALA A:138 , HIS A:142 , ARG A:220BINDING SITE FOR RESIDUE SCN A1266

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V3U)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:13 -Pro A:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V3U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V3U)

(-) Exons   (0, 0)

(no "Exon" information available for 2V3U)

(-) 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:253
 aligned with GRID2_RAT | Q63226 from UniProtKB/Swiss-Prot  Length:1007

    Alignment length:371
                                   448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808 
            GRID2_RAT   439 RGVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRRAEKTVDMFACLAPFDLSLWACIAGTVLLVGLLVYLLNWLNPPRLQMGSMTSTTLYNSMWFVYGSFVQQGGEVPYTTLATRMMMGAWWLFALIVISSYTANLAAFLTITRIESSIQSLQDLSKQTDIPYGTVLDSAVYQHVRMKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRILELQQSGDMDILKHKWWPKNG 809
               SCOP domains d2v3ua_ A: automated matches                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2v3uA01 A:1-105,A:220-261 Periplasmic binding protein-like II                                            --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2v3uA01 A:1-105,A:220-261                  CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------                                                                                                              Lig_chan-2v3uA01 A:115-261                                                                                                                          Pfam domains (1)
           Pfam domains (2) ----SBP_bac_3-2v3uA02 A:5-259                                                                                                                                                                                                                                                                                                                                                    -- Pfam domains (2)
         Sec.struct. author ...eeeeee.......eee........eeehhhhhhhhhhhhhhh.eeeeee...............hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee..--------------------------------------------------------------------------------------------------------------....hhhhhhh.....ee....hhhhhhhhhhhh......hhhhhhhhhhh.-----....hhhhhhhhhhhh..eeeeehhhhhhhhhhh....eeee.---..eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v3u A   1 GGVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRRG--------------------------------------------------------------------------------------------------------------TSIQSLQDLSKQTDIPYGTVLDSAVYQHVRMKGLNPFERDSMYSQMWRMINR-----NNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFYTVG---ADRGYGIALQHGSPYRDVFSQRILELQQSGDMDILKHKWWPKNG 261
                                    10        20        30        40        50        60        70        80        90       100       110   |     -         -         -         -         -         -         -         -         -         -         -    |  120       130       140       150       160     |   - |     180       190       200       210   |   220       230       240       250       260 
                                                                                                                                           114                                                                                                            115                                                166   172                                       214 218                                           

   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/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GRID2_RAT | Q63226)
molecular function
    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:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0034613    cellular protein localization    Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
    GO:0021707    cerebellar granule cell differentiation    The process in which neuroblasts acquire specialized structural and/or functional features that characterize the mature cerebellar granule cell. Differentiation includes the processes involved in commitment of a neuroblast to a granule cell fate. A granule cell is a glutamatergic interneuron found in the cerebellar cortex.
    GO:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
    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: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: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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GRID2_RAT | Q632262v3t 5cc2 5l2e

(-) Related Entries Specified in the PDB File

2v3t STRUCTURE OF THE LIGAND-BINDING CORE OF THE IONOTROPIC GLUTAMATE RECEPTOR-LIKE GLURDELTA2 IN THE APO FORM