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(-) Description

Title :  CRYSTAL STRUCTURE OF TAMALIN PDZ DOMAIN
 
Authors :  T. Sugi, T. Oyama, T. Muto, S. Nakanishi, K. Morikawa, H. Jingami
Date :  01 Mar 07  (Deposition) - 01 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pdz Domain, Ligand-Free, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Sugi, T. Oyama, T. Muto, S. Nakanishi, K. Morikawa, H. Jingami
Crystal Structures Of Autoinhibitory Pdz Domain Of Tamalin: Implications For Metabotropic Glutamate Receptor Trafficking Regulation
Embo J. V. 26 2192 2007
PubMed-ID: 17396155  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601651
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GENERAL RECEPTOR FOR PHOSPHOINOSITIDES 1- ASSOCIATED SCAFFOLD PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX4T-1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN
    MutationYES
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymGRP1-ASSOCIATED SCAFFOLD PROTEIN, TAMALIN, 95 KDA POSTSYNAPTIC DENSITY PROTEIN DISCS-LARGE ZO-1 DOMAIN- CONTAINING PROTEIN, PSD-95 PDZ DOMAIN-CONTAINING PROTEIN
    TissueBRAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2EGO)

(-) Sites  (0, 0)

(no "Site" information available for 2EGO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EGO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.GRASP_RAT100-189
 
  2A:100-189
B:100-189

(-) Exons   (5, 10)

Asymmetric/Biological Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000099791ENSRNOE00000067795chr7:139970173-139970475303GRASP_RAT1-81810--
1.2ENSRNOT000000099792ENSRNOE00000068177chr7:139972477-13997252650GRASP_RAT82-98172A:95-98
B:95-98
4
4
1.3ENSRNOT000000099793ENSRNOE00000068453chr7:139974479-13997453355GRASP_RAT98-116192A:98-116
B:98-116
19
19
1.4ENSRNOT000000099794ENSRNOE00000068702chr7:139974634-139974736103GRASP_RAT117-151352A:117-151 (gaps)
B:117-151 (gaps)
35
35
1.5ENSRNOT000000099795ENSRNOE00000068932chr7:139976099-13997619294GRASP_RAT151-182322A:151-182
B:151-182
32
32
1.6ENSRNOT000000099796ENSRNOE00000069212chr7:139976301-13997636767GRASP_RAT182-204232A:182-189
B:182-189
8
8
1.7ENSRNOT000000099797ENSRNOE00000069501chr7:139976562-13997662867GRASP_RAT205-227230--
1.8ENSRNOT000000099798ENSRNOE00000069773chr7:139977213-139977939727GRASP_RAT227-3941680--

(-) 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:88
 aligned with GRASP_RAT | Q8R4T5 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:95
                                   104       114       124       134       144       154       164       174       184     
            GRASP_RAT    95 EQQRKVLTLEKGDNQTFGFEIQTYGLHHREEQRVEMVTFVCRVHESSPAQLAGLTPGDTIASVNGLNVEGIRHREIVDIIKASGNVLRLETLYGT 189
               SCOP domains d2egoa_ A: automated match       es                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee........eeeeeee.-------..eeeeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhhh..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: A:100-189 UniProt: 100-189                                                       PROSITE
           Transcript 1 (1) 1.2 ------------------Exon 1.4  PDB: A:117-151 (gaps)    ------------------------------Exon 1.6 Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.3           ----------------------------------Exon 1.5  PDB: A:151-182        ------- Transcript 1 (2)
                 2ego A  95 SQQRKVLTLEKGDNQTFGFEIQTYGL-------VEMVTFVARVHESSPAQLAGLTPGDTIASVNGLNVEGIRHREIVDIIKASGNVLRLETLYGT 189
                                   104       114     |   -   |   134       144       154       164       174       184     
                                                   120     128                                                             

Chain B from PDB  Type:PROTEIN  Length:90
 aligned with GRASP_RAT | Q8R4T5 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:95
                                   104       114       124       134       144       154       164       174       184     
            GRASP_RAT    95 EQQRKVLTLEKGDNQTFGFEIQTYGLHHREEQRVEMVTFVCRVHESSPAQLAGLTPGDTIASVNGLNVEGIRHREIVDIIKASGNVLRLETLYGT 189
               SCOP domains d2egob_ B: automated matches                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee........eeeeeeee..-----.eeeeeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhhhh..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: B:100-189 UniProt: 100-189                                                       PROSITE
           Transcript 1 (1) 1.2 ------------------Exon 1.4  PDB: B:117-151 (gaps)    ------------------------------Exon 1.6 Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.3           ----------------------------------Exon 1.5  PDB: B:151-182        ------- Transcript 1 (2)
                 2ego B  95 SQQRKVLTLEKGDNQTFGFEIQTYGLHH-----VEMVTFVARVHESSPAQLAGLTPGDTIASVNGLNVEGIRHREIVDIIKASGNVLRLETLYGT 189
                                   104       114       | -   |   134       144       154       164       174       184     
                                                     122   128                                                             

   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 2EGO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EGO)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GRASP_RAT | Q8R4T5)
molecular function
    GO:0030306    ADP-ribosylation factor binding    Interacting selectively and non-covalently with ARF, ADP-ribosylation factor, a small monomeric cytosolic GTPase that, when bound to GTP, binds to the membranes of cells.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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).
biological process
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    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.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GRASP_RAT | Q8R4T52egk 2egn

(-) Related Entries Specified in the PDB File

2egk TAMALIN PDZ-INTRINSIC LIGAND FUSION PROTEIN
2egn TAMALIN PDZ DOMAIN IN COMPLEX WITH MGLUR5 C-TERMINAL PEPTIDE