Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE THIRD PDZ DOMAIN OF SYNAPSE-ASSOCIATED PROTEIN 102
 
Authors :  X. -R. Qin, T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  24 Sep 03  (Deposition) - 24 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pdz, Discs Large Homolog 3, Dlg3-Human Presynaptic Protein, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. -R. Qin, T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of The Third Pdz Domain Of Synapse-Associated Protein 102
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SYNAPSE-ASSOCIATED PROTEIN 102
    ChainsA
    EngineeredYES
    Expression System PlasmidP021030-42
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN
    GeneKAZUSA CDNA KIAA1232
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymKIAA1232 PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1UM7)

(-) Sites  (0, 0)

(no "Site" information available for 1UM7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UM7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UM7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UM7)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DLG3_HUMAN131-218
226-313
386-467
  1-
-
A:18-99
2SH3PS50002 Src homology 3 (SH3) domain profile.DLG3_HUMAN501-571  1A:110-113

(-) Exons   (7, 7)

NMR Structure (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003743601bENSE00001958108X:69664819-69665408590DLG3_HUMAN1-1191190--
1.3ENST000003743603ENSE00000672255X:69668763-6966881351DLG3_HUMAN120-136170--
1.4ENST000003743604ENSE00000672253X:69669209-69669333125DLG3_HUMAN137-178420--
1.5ENST000003743605ENSE00000672252X:69669540-69669709170DLG3_HUMAN178-235580--
1.6aENST000003743606aENSE00000436378X:69670019-69670155137DLG3_HUMAN235-280461A:1-88
1.6cENST000003743606cENSE00000672250X:69670489-69670633145DLG3_HUMAN281-329491A:9-102
1.7ENST000003743607ENSE00000672249X:69671717-69671876160DLG3_HUMAN329-382541A:11-14 (gaps)49
1.9ENST000003743609ENSE00001599030X:69673487-69673643157DLG3_HUMAN382-434531A:14-6653
1.10ENST0000037436010ENSE00000672247X:69674064-69674166103DLG3_HUMAN435-469351A:67-10135
1.13bENST0000037436013bENSE00001675478X:69699000-69699114115DLG3_HUMAN469-507391A:101-109 (gaps)24
1.14bENST0000037436014bENSE00000672235X:69711957-69712133177DLG3_HUMAN507-566601A:110-1134
1.15ENST0000037436015ENSE00000436409X:69712371-6971244676DLG3_HUMAN566-591260--
1.17ENST0000037436017ENSE00000815626X:69715258-6971530346DLG3_HUMAN592-607160--
1.19bENST0000037436019bENSE00000672149X:69718370-6971842051DLG3_HUMAN607-624180--
1.20ENST0000037436020ENSE00001705646X:69719026-69719127102DLG3_HUMAN624-658350--
1.21bENST0000037436021bENSE00000672147X:69719727-69719899173DLG3_HUMAN658-715580--
1.22aENST0000037436022aENSE00000672146X:69720321-69720430110DLG3_HUMAN716-752370--
1.22cENST0000037436022cENSE00000436391X:69720748-6972083992DLG3_HUMAN752-783320--
1.23cENST0000037436023cENSE00001154826X:69722013-697253373325DLG3_HUMAN783-817350--

(-) Sequences/Alignments

NMR Structure
   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:113
 aligned with DLG3_HUMAN | Q92796 from UniProtKB/Swiss-Prot  Length:817

    Alignment length:261
                                   273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523 
           DLG3_HUMAN   264 GAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPGSLHLNDMYAPPDYASTFTALADNHISHNSSLGYLGAVESKVSYPAPPQVPPTRYSPIPRHMLAEEDFTREPRKIILHKGSTGLGFNIVGGEDGEGIFVSFILAGGPADLSGELRRGDRILSVNGVNLRNATHEQAAAALKRAGQSVTIVAQYRPEEYSRFESKIHDLREQMMNSSMSSGSGSLRTSEKRSLYVRALFDYDRTRDSCLPSQG 524
               SCOP domains d1um7a_                                         A:                     S                                             ynapse-associated protein 102                                                                                                                    SCOP domains
               CATH domains 1um7A00                                         A:                    1-                                             113  [code=2.30.42.10, no name defined]                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------PDZ_PDZ-1um7A01 A:18-96                                                            ------------------------------------------------------------ Pfam domains
         Sec.struct. author ........----------------------------------------..--------------------..---------------------------------------------...eeeeeee...........................hhhhhh.......eeeee........hhhhhhhhhhh...eeeeeee.hhhhhhhhh---------------hh.----------------------------.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PDZ  PDB: - UniProt: 226-313                      ------------------------------------------------------------------------PDZ  PDB: A:18-99 UniProt: 386-467                                                ---------------------------------SH3  PDB: A:110-113      PROSITE
           Transcript 1 (1) Exon 1.6a        Exon 1.6c  PDB: A:9-10 UniProt: 281-329          ----------------------------------------------------Exon 1.9  PDB: A:14-66 UniProt: 382-434              Exon 1.10  PDB: A:67-101           -------------------------------------Exon 1.14b         Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------Exon 1.7  PDB: A:11-14 (gaps) UniProt: 329-382        --------------------------------------------------------------------------------------Exon 1.13b  PDB: A:101-109 (gaps)      ----------------- Transcript 1 (2)
                 1um7 A   1 GSSGSSGR----------------------------------------PG--------------------GD---------------------------------------------AREPRKIILHKGSTGLGFNIVGGEDGEGIFVSFILAGGPADLSGELRRGDRILSVNGVNLRNATHEQAAAALKRAGQSVTIVAQYRPEEYSRFE---------------SSG----------------------------PSSG 113
                                   | -         -         -         -        10         -         -||       -         -         -         -       |15        25        35        45        55        65        75        85        95       105|        -      | |-         -         -       112 
                                   8                                        9|                   11|                                            13                                                                                          106             107 |                          110   
                                                                            10                    12                                                                                                                                                          109                                

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

NMR Structure
(-)
Clan: PDZ-like (184)

(-) Gene Ontology  (36, 36)

NMR Structure(hide GO term definitions)
Chain A   (DLG3_HUMAN | Q92796)
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:0004385    guanylate kinase activity    Catalysis of the reaction: ATP + GMP = ADP + GDP.
    GO:0035255    ionotropic glutamate receptor binding    Interacting selectively and non-covalently with an ionotropic glutamate receptor. Ionotropic glutamate receptors bind glutamate and exert an effect through the regulation of ion channels.
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    GO:0015276    ligand-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.
    GO:0019902    phosphatase binding    Interacting selectively and non-covalently with any phosphatase.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0046710    GDP metabolic process    The chemical reactions and pathways involving GDP, guanosine 5'-diphosphate.
    GO:0046037    GMP metabolic process    The chemical reactions and pathways involving GMP, guanosine monophosphate.
    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:0001736    establishment of planar polarity    Coordinated organization of groups of cells in the plane of an epithelium, such that they all orient to similar coordinates.
    GO:0045197    establishment or maintenance of epithelial cell apical/basal polarity    Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of an epithelial 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:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0010923    negative regulation of phosphatase activity    Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    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:0043113    receptor clustering    The receptor metabolic process that results in grouping of a set of receptors at a cellular location, often to amplify the sensitivity of a signaling response.
    GO:0097120    receptor localization to synapse    Any process in which a receptor is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.
cellular component
    GO:0032281    AMPA glutamate receptor complex    An 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. The AMPA receptors mediate fast synaptic transmission in the CNS and are composed of subunits GluR1-4, products from separate genes. These subunits have an extracellular N-terminus and an intracellular C-terminus.
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0005923    bicellular tight junction    An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043198    dendritic shaft    Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    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: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: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.

 Visualization

(-) Interactive Views

NMR Structure
  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 1um7)
 
  Sites
(no "Sites" information available for 1um7)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1um7)
 

(-) 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
  1um7
    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
  DLG3_HUMAN | Q92796
    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
  DLG3_HUMAN | Q92796
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DLG3_HUMAN | Q927962fe5 2i1n

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1UM7)