Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF TAMALIN PDZ DOMAIN IN COMPLEX WITH MGLUR5 C-TERMINAL PEPTIDE
 
Authors :  T. Sugi, T. Oyama, T. Muto, S. Nakanishi, K. Morikawa, H. Jingami
Date :  01 Mar 07  (Deposition) - 15 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Pdz Domain, Peptide Complex, 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
    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
 
Molecule 2 - MGLUR5 C-TERMINAL PEPTIDE
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX4T-1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    Other DetailsPDZ DOMAIN-MGLUR5 GENE CO-EXPRESSED AS C- TERMINUS FUSION PROTEIN IN E.COLI.

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2EGN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

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

(-) Exons   (5, 5)

Asymmetric Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000099791ENSRNOE00000067795chr7:139970173-139970475303GRASP_RAT1-81810--
1.2ENSRNOT000000099792ENSRNOE00000068177chr7:139972477-13997252650GRASP_RAT82-98171A:96-983
1.3ENSRNOT000000099793ENSRNOE00000068453chr7:139974479-13997453355GRASP_RAT98-116191A:98-11619
1.4ENSRNOT000000099794ENSRNOE00000068702chr7:139974634-139974736103GRASP_RAT117-151351A:117-151 (gaps)35
1.5ENSRNOT000000099795ENSRNOE00000068932chr7:139976099-13997619294GRASP_RAT151-182321A:151-18232
1.6ENSRNOT000000099796ENSRNOE00000069212chr7:139976301-13997636767GRASP_RAT182-204231A:182-1898
1.7ENSRNOT000000099797ENSRNOE00000069501chr7:139976562-13997662867GRASP_RAT205-227230--
1.8ENSRNOT000000099798ENSRNOE00000069773chr7:139977213-139977939727GRASP_RAT227-3941680--

(-) 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:83
 aligned with GRASP_RAT | Q8R4T5 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:94
                                   105       115       125       135       145       155       165       175       185    
            GRASP_RAT    96 QQRKVLTLEKGDNQTFGFEIQTYGLHHREEQRVEMVTFVCRVHESSPAQLAGLTPGDTIASVNGLNVEGIRHREIVDIIKASGNVLRLETLYGT 189
               SCOP domains d2egna_ A: automated mat           ches                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee........eeeee..-----------.eeeeee...hhhhhhh....eeeeee..ee....hhhhhhhhhhh...eeeeeeee.. 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)
                 2egn A  96 QQRKVLTLEKGDNQTFGFEIQTYG-----------VTFVARVHESSPAQLAGLTPGDTIASVNGLNVEGIRHREIVDIIKASGNVLRLETLYGT 189
                                   105       115   |     -     | 135       145       155       165       175       185    
                                                 119         131                                                          

Chain B from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 2egn B 190 SSSSL 194

   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 2EGN)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2egn)
 
  Sites
(no "Sites" information available for 2egn)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2egn)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2egn
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GRASP_RAT | Q8R4T5
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  GRASP_RAT | Q8R4T5
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GRASP_RAT | Q8R4T52egk 2ego

(-) Related Entries Specified in the PDB File

2egk TAMALIN PDZ-INTRINSIC LIGAND FUSION PROTEIN
2ego TAMALIN PDZ DOMAIN