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(-) Description

Title :  SOLUTION STRUCTURE OF THE SECOND PDZ DOMAIN OF HUMAN SCRIBBLE (KIAA0147 PROTEIN).
 
Authors :  N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pdz Domain, Cellular Signaling, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Second Pdz Domain Of Human Scribble (Kiaa0147 Protein).
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KIAA0147 PROTEIN
    ChainsA
    EngineeredYES
    Expression System PlasmidP021030-56
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN
    GeneKAZUSA CDNA HA01022S1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymSCRIBBLE

 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 1WHA)

(-) Sites  (0, 0)

(no "Site" information available for 1WHA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.SCRIB_HUMAN728-815
862-950
1004-1093
1100-1188
  1-
A:10-98
-
-

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003204761ENSE00001421242chr8:144897549-144897384166SCRIB_HUMAN1-53530--
1.3ENST000003204763ENSE00001710051chr8:144896288-144896171118SCRIB_HUMAN54-93400--
1.4ENST000003204764ENSE00001280634chr8:144896066-14489598879SCRIB_HUMAN93-119270--
1.5ENST000003204765ENSE00001280624chr8:144895896-14489580790SCRIB_HUMAN119-149310--
1.6ENST000003204766ENSE00001280614chr8:144895696-14489564057SCRIB_HUMAN149-168200--
1.7ENST000003204767ENSE00001280605chr8:144895544-14489548164SCRIB_HUMAN168-189220--
1.8ENST000003204768ENSE00001280596chr8:144895274-14489520075SCRIB_HUMAN190-214250--
1.9ENST000003204769ENSE00001280589chr8:144895131-144894987145SCRIB_HUMAN215-263490--
1.10ENST0000032047610ENSE00001280580chr8:144894554-144894436119SCRIB_HUMAN263-302400--
1.11ENST0000032047611ENSE00001280573chr8:144893515-144893316200SCRIB_HUMAN303-369670--
1.12ENST0000032047612ENSE00001280566chr8:144893242-144893076167SCRIB_HUMAN369-425570--
1.13ENST0000032047613ENSE00001280559chr8:144892986-144892856131SCRIB_HUMAN425-468440--
1.14ENST0000032047614ENSE00001280549chr8:144892774-144892649126SCRIB_HUMAN469-510420--
1.15ENST0000032047615ENSE00001280543chr8:144891888-144891721168SCRIB_HUMAN511-566560--
1.16aENST0000032047616aENSE00001280537chr8:144891195-144890779417SCRIB_HUMAN567-7051390--
1.17ENST0000032047617ENSE00001280531chr8:144889784-14488972263SCRIB_HUMAN706-726210--
1.18ENST0000032047618ENSE00001280522chr8:144889183-14488909490SCRIB_HUMAN727-756300--
1.19ENST0000032047619ENSE00001280512chr8:144888654-14488857778SCRIB_HUMAN757-782260--
1.20bENST0000032047620bENSE00001280505chr8:144887605-144887282324SCRIB_HUMAN783-8901081A:1-38 (gaps)48
1.21ENST0000032047621ENSE00001280498chr8:144887184-14488710481SCRIB_HUMAN891-917271A:39-6527
1.22ENST0000032047622ENSE00001280489chr8:144886995-144886738258SCRIB_HUMAN918-1003861A:66-105 (gaps)50
1.23aENST0000032047623aENSE00001280482chr8:144886326-144886216111SCRIB_HUMAN1004-1040370--
1.24ENST0000032047624ENSE00001280475chr8:144886110-144885817294SCRIB_HUMAN1041-1138980--
1.25ENST0000032047625ENSE00001280467chr8:144885741-144885553189SCRIB_HUMAN1139-1201630--
1.26ENST0000032047626ENSE00001280460chr8:144877700-144877590111SCRIB_HUMAN1202-1238370--
1.27ENST0000032047627ENSE00001280713chr8:144877503-14487744757SCRIB_HUMAN1239-1257190--
1.28ENST0000032047628ENSE00001280704chr8:144877282-14487720875SCRIB_HUMAN1258-1282250--
1.29ENST0000032047629ENSE00001280697chr8:144876132-14487607063SCRIB_HUMAN1283-1303210--
1.30bENST0000032047630bENSE00001280801chr8:144875253-144875146108SCRIB_HUMAN1304-1339360--
1.31aENST0000032047631aENSE00001280748chr8:144875037-144874878160SCRIB_HUMAN1340-1393540--
1.31cENST0000032047631cENSE00001280742chr8:144874805-144874655151SCRIB_HUMAN1393-1443510--
1.32aENST0000032047632aENSE00001280685chr8:144874575-144874390186SCRIB_HUMAN1443-1505630--
1.33ENST0000032047633ENSE00001280794chr8:144874303-144874161143SCRIB_HUMAN1505-1553490--
1.34ENST0000032047634ENSE00001280669chr8:144874083-14487404638SCRIB_HUMAN1553-1565130--
1.36bENST0000032047636bENSE00001346693chr8:144873610-14487355952SCRIB_HUMAN1566-1583180--
1.37cENST0000032047637cENSE00001280723chr8:144873478-144873090389SCRIB_HUMAN1583-1630480--

(-) 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:105
 aligned with SCRIB_HUMAN | Q14160 from UniProtKB/Swiss-Prot  Length:1630

    Alignment length:125
                                   852       862       872       882       892       902       912       922       932       942       952       962     
          SCRIB_HUMAN   843 GLRLPLLPPESPGPLRQRHVACLARSERGLGFSIAGGKGSTPYRAGDAGIFVSRIAEGGAAHRAGTLQVGDRVLSINGVDVTEARHDHAVSLLTAASPTIALLLEREAGGPLPPSPLPHSSPPTA 967
               SCOP domains d      1whaa_     A: Scribble (KIAA0147)                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------PDZ-1whaA01 A:12-95                                                                 -------------------- Pfam domains
         Sec.struct. author .------.....e----eeeeee.........eee...............eeee.....hhhhhh......eeeee........hhhhhhhhhh.....eeeeeee...----------...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------PDZ  PDB: A:10-98 UniProt: 862-950                                                       ----------------- PROSITE
               Transcript 1 Exon 1.20b  PDB: A:1-38 (gaps) UniProt: 783-890 Exon 1.21  PDB: A:39-65    Exon 1.22  PDB: A:66-105 (gaps) UniProt: 918-1003  Transcript 1
                 1wha A   1 G------SSGSSG----RHVACLARSERGLGFSIAGGKGSTPYRAGDAGIFVSRIAEGGAAHRAGTLQVGDRVLSINGVDVTEARHDHAVSLLTAASPTIALLLEREAG----------SGPSSG 105
                            |      | 4  |    |10        20        30        40        50        60        70        80        90        |-       100     
                            |      2    7    8                                                                                         99        100     
                            1                                                                                                                            

   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  (0, 0)

(no "CATH Domain" information available for 1WHA)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (45, 45)

NMR Structure(hide GO term definitions)
Chain A   (SCRIB_HUMAN | Q14160)
molecular function
    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:0090630    activation of GTPase activity    Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
    GO:0060561    apoptotic process involved in morphogenesis    Any apoptotic process that contributes to the shaping of an anatomical structure.
    GO:0043615    astrocyte cell migration    The orderly movement of an astrocyte, a class of large neuroglial (macroglial) cells in the central nervous system, the largest and most numerous neuroglial cells in the brain and spinal cord.
    GO:0008105    asymmetric protein localization    Any process in which a protein is transported to, or maintained in, a specific location such that it is distributed asymmetrically.
    GO:0002093    auditory receptor cell morphogenesis    Any process that alters the size or shape of an auditory receptor cell.
    GO:0060088    auditory receptor cell stereocilium organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a stereocilium. A stereocilium is an actin-based protrusion from the apical surface of auditory hair cells.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0021747    cochlear nucleus development    The process whose specific outcome is the progression of the cochlear nucleus over time, from its formation to the mature structure.
    GO:0035089    establishment of apical/basal cell polarity    The specification and formation of the polarity of a cell along its apical/basal axis.
    GO:0060603    mammary gland duct morphogenesis    The process in which anatomical structures of the mammary ducts are generated and organized. Mammary ducts are epithelial tubes that transport milk.
    GO:0016331    morphogenesis of embryonic epithelium    The process in which the anatomical structures of embryonic epithelia are generated and organized.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0045930    negative regulation of mitotic cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle.
    GO:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    GO:0050918    positive chemotaxis    The directed movement of a motile cell or organism towards a higher concentration of a chemical.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0001921    positive regulation of receptor recycling    Any process that activates or increases the frequency, rate or extent of receptor recycling.
    GO:0071896    protein localization to adherens junction    Any process in which a protein is transported to, and/or maintained at the adherens junction.
    GO:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
    GO:0048488    synaptic vesicle endocytosis    Clathrin-mediated endocytosis of presynaptic membrane that recycles synaptic vesicle membrane and its components following synaptic vesicle exocytosis. This process starts with coating of the membrane with adaptor proteins and clathrin prior to invagination and ends when uncoating has finished.
    GO:0016080    synaptic vesicle targeting    The process in which synaptic vesicles are directed to specific destination membranes, mediated by molecules at the vesicle membrane and target membrane surfaces.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0034750    Scrib-APC-beta-catenin complex    A protein complex that contains the Scribble protein (a cell polarity determinant), the tumor suppressor protein adenomatous polyposis coli (APC), and beta-catenin; may be involved in the control of cell proliferation.
    GO:0005912    adherens junction    A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
    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: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:0031252    cell leading edge    The area of a motile cell closest to the direction of movement.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005913    cell-cell adherens junction    An adherens junction which connects a cell to another cell.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0035748    myelin sheath abaxonal region    The region of the myelin sheath furthest from the axon.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0098793    presynapse    The part of a synapse that is part of the presynaptic cell.
    GO:0042734    presynaptic membrane    A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SCRIB_HUMAN | Q141601uju 1x5q 2w4f 4wyt 4wyu

(-) Related Entries Specified in the PDB File

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