Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF TAMALIN PDZ-INTRINSIC LIGAND FUSION PROTEIN
 
Authors :  T. Sugi, T. Oyama, T. Muto, S. Nakanishi, K. Morikawa, H. Jingami
Date :  01 Mar 07  (Deposition) - 08 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Pdz Domain, Ligand Fusion, 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, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX4T-1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN, C-TERMINAL PEPTODE(INTRINSIC LIGAND)
    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

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD
Biological Unit 3 (1x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:168 , PO4 B:195 , HOH C:21 , ARG C:166 , HIS C:167 , ARG C:168 , GLU D:191BINDING SITE FOR RESIDUE PO4 C 195
2AC2SOFTWAREHIS B:167 , ARG B:168 , HIS C:167 , PO4 C:195BINDING SITE FOR RESIDUE PO4 B 195

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.GRASP_RAT100-189
 
 
 
  4A:100-189
B:100-187
C:100-187
D:100-189
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.GRASP_RAT100-189
 
 
 
  2A:100-189
B:100-187
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.GRASP_RAT100-189
 
 
 
  2-
-
C:100-187
D:100-189
Biological Unit 3 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.GRASP_RAT100-189
 
 
 
  4A:100-189
B:100-187
C:100-187
D:100-189

(-) Exons   (6, 22)

Asymmetric Unit (6, 22)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000099791ENSRNOE00000067795chr7:139970173-139970475303GRASP_RAT1-81810--
1.2ENSRNOT000000099792ENSRNOE00000068177chr7:139972477-13997252650GRASP_RAT82-98174A:97-98
B:97-98
C:98-98
D:98-98
2
2
1
1
1.3ENSRNOT000000099793ENSRNOE00000068453chr7:139974479-13997453355GRASP_RAT98-116194A:98-116
B:98-116
C:98-116
D:98-116
19
19
19
19
1.4ENSRNOT000000099794ENSRNOE00000068702chr7:139974634-139974736103GRASP_RAT117-151354A:117-151 (gaps)
B:117-151 (gaps)
C:117-151 (gaps)
D:117-151 (gaps)
35
35
35
35
1.5ENSRNOT000000099795ENSRNOE00000068932chr7:139976099-13997619294GRASP_RAT151-182324A:151-182
B:151-182
C:151-182
D:151-182
32
32
32
32
1.6ENSRNOT000000099796ENSRNOE00000069212chr7:139976301-13997636767GRASP_RAT182-204234A:182-189
B:182-194 (gaps)
C:182-194 (gaps)
D:182-189
8
19
19
8
1.7ENSRNOT000000099797ENSRNOE00000069501chr7:139976562-13997662867GRASP_RAT205-227232A:190-194
-
-
D:190-194
5
-
-
5
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:89
 aligned with GRASP_RAT | Q8R4T5 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:128
                                   106       116       126       136       146       156       166       176       186       196       206       216        
            GRASP_RAT    97 QRKVLTLEKGDNQTFGFEIQTYGLHHREEQRVEMVTFVCRVHESSPAQLAGLTPGDTIASVNGLNVEGIRHREIVDIIKASGNVLRLETLYGTSIRKAELEARLQYLKQTLYEKWGEYRSLMVQEQRL 224
               SCOP domains d2egka_ A: automated mat         ches                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........eeeeee..---------.eeeeeee...hhhhhh......eeeee........hhhhhhhhhhhh..eeeeeee..e------------------------------e.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PDZ  PDB: A:100-189 UniProt: 100-189                                                      ----------------------------------- PROSITE
           Transcript 1 (1) 1.------------------Exon 1.4  PDB: A:117-151 (gaps)    ------------------------------Exon 1.6  PDB: A:182-18Exon 1.7             Transcript 1 (1)
           Transcript 1 (2) -Exon 1.3           ----------------------------------Exon 1.5  PDB: A:151-182        ------------------------------------------ Transcript 1 (2)
                 2egk A  97 QRKVLTLEKGDNQTFGFEIQTYGL---------mVTFVARVHESSPAQLAGLTPGDTIASVNGLNVEGIRHREIVDIIKASGNVLRLETLYGT------------------------------EESQL 194
                                   106       116   |     -   |   136       146       156       166       176       186  |      -         -         -   |    
                                                 120       130-MSE                                                    189                            190    

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

    Alignment length:104
                                   106       116       126       136       146       156       166       176       186       196    
            GRASP_RAT    97 QRKVLTLEKGDNQTFGFEIQTYGLHHREEQRVEMVTFVCRVHESSPAQLAGLTPGDTIASVNGLNVEGIRHREIVDIIKASGNVLRLETLYGTSIRKAELEARL 200
               SCOP domains d2egkb_ B: automated match     es                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........eeeeeeee..-----.eeeeeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeee.---------.ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PDZ  PDB: B:100-187 UniProt: 100-189                                                      ----------- PROSITE
           Transcript 1 (1) 1.------------------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)
                 2egk B  97 QRKVLTLEKGDNQTFGFEIQTYGLHH-----VEmVTFVARVHESSPAQLAGLTPGDTIASVNGLNVEGIRHREIVDIIKASGNVLRLETLY---------ESQL 194
                                   106       116     |   - | |   136       146       156       166       176       186|        -|   
                                                   122   128 |                                                      187       191   
                                                           130-MSE                                                                  

Chain C from PDB  Type:PROTEIN  Length:88
 aligned with GRASP_RAT | Q8R4T5 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:103
                                   107       117       127       137       147       157       167       177       187       197   
            GRASP_RAT    98 RKVLTLEKGDNQTFGFEIQTYGLHHREEQRVEMVTFVCRVHESSPAQLAGLTPGDTIASVNGLNVEGIRHREIVDIIKASGNVLRLETLYGTSIRKAELEARL 200
               SCOP domains d2egkc_ C: automated mat      ches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee........eeeeeeee.------.eeeeeeeee...hhhhhh.........ee..ee....hhhhhhhhhhh...eeeee...---------.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --PDZ  PDB: C:100-187 UniProt: 100-189                                                      ----------- PROSITE
           Transcript 1 (1) 1------------------Exon 1.4  PDB: C:117-151 (gaps)    ------------------------------Exon 1.6            Transcript 1 (1)
           Transcript 1 (2) Exon 1.3           ----------------------------------Exon 1.5  PDB: C:151-182        ------------------ Transcript 1 (2)
                 2egk C  98 RKVLTLEKGDNQTFGFEIQTYGLH------VEmVTFVARVHESSPAQLAGLTPGDTIASVNGLNVEGIRHREIVDIIKASGNVLRLETLY---------ESQL 194
                                   107       117   |     -| |    137       147       157       167       177       187       191   
                                                 121    128 |                                                      187       191   
                                                          130-MSE                                                                  

Chain D from PDB  Type:PROTEIN  Length:87
 aligned with GRASP_RAT | Q8R4T5 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:127
                                   107       117       127       137       147       157       167       177       187       197       207       217       
            GRASP_RAT    98 RKVLTLEKGDNQTFGFEIQTYGLHHREEQRVEMVTFVCRVHESSPAQLAGLTPGDTIASVNGLNVEGIRHREIVDIIKASGNVLRLETLYGTSIRKAELEARLQYLKQTLYEKWGEYRSLMVQEQRL 224
               SCOP domains d2egkd_ D: automated m          atches                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........eeeeee.----------.eeeeeee...hhhhhh......eeeee........hhhhhhhhhhh...eeeeeee..e------------------------------e.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --PDZ  PDB: D:100-189 UniProt: 100-189                                                      ----------------------------------- PROSITE
           Transcript 1 (1) 1------------------Exon 1.4  PDB: D:117-151 (gaps)    ------------------------------Exon 1.6  PDB: D:182-18Exon 1.7             Transcript 1 (1)
           Transcript 1 (2) Exon 1.3           ----------------------------------Exon 1.5  PDB: D:151-182        ------------------------------------------ Transcript 1 (2)
                 2egk D  98 RKVLTLEKGDNQTFGFEIQTYG----------mVTFVARVHESSPAQLAGLTPGDTIASVNGLNVEGIRHREIVDIIKASGNVLRLETLYGT------------------------------EESQL 194
                                   107       117 |       -  |    137       147       157       167       177       187 |       -         -         -  |    
                                               119        130-MSE                                                    189                            190    

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2EGK)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2egk)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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
  2egk
    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 | Q8R4T52egn 2ego

(-) Related Entries Specified in the PDB File

2egn TAMALIN PDZ DOMAIN IN COMPLEX WITH MGLUR5 C-TERMINAL PEPTIDE
2ego TAMALIN PDZ DOMAIN