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(-) Description

Authors :  H. Abe, N. Tochio, K. Miyamoto, K. Saito, A. Sasagawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 Apr 07  (Deposition) - 09 Oct 07  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Sorbin And Sh3 Domain-Containing Protein 3, Sh3-Containing Adapter Molecule 1, Scam-1, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  H. Abe, N. Tochio, K. Miyamoto, K. Saito, A. Sasagawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Second Sh3 Domain Of Human Vinexin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VINEXIN
    Expression System PlasmidP050627-09
    Expression System Vector TypePLASMID
    FragmentSH3 DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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 2YUP)

(-) Sites  (0, 0)

(no "Site" information available for 2YUP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
1SH3PS50002 Src homology 3 (SH3) domain profile.VINEX_HUMAN380-439

(-) Exons   (4, 4)

NMR Structure (4, 4)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.19cENST0000024012319cENSE00001667727chr8:22428423-22428734312VINEX_HUMAN478-5811041A:39-90 (gaps)82

(-) 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:90
 aligned with VINEX_HUMAN | O60504 from UniProtKB/Swiss-Prot  Length:671

    Alignment length:213
                                   356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556   
               SCOP domains d2                 yupa_                                                                             A: automated matches                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------2yupA01 A:13-77 SH3 Domains                                      ------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------SH3_1-2yupA01 A:21-68                           ---------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------------.....----------------------------------------------------------------------------.....hhhhheeeee..................eeee.......eeeee......eeeee...eeeee.........---------------..--...-------------. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------SH3  PDB: - UniProt: 380-439                                --------------SH3  PDB: A:15-76 UniProt: 454-515                            -------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.15h        -----------------Exon 1.16e      --------------------------------------Exon 1.18b  PDB: A:8-38 UniProt: 436-477  Exon 1.19c  PDB: A:39-90 (gaps) UniProt: 478-581 [INCOMPLETE]                      Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.16b        ---------------Exon 1.17c  PDB: - UniProt: 397-435    ---------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2yup A   1 GS-----------------SGSSG----------------------------------------------------------------------------KPPTYQVLEYGEAVAQYTFKGDLEVELSFRKGEHICLIRKVNENWYEGRITGTGRQGIFPASYVQVSREPRLRLCDD---------------SG--PSS-------------G  90
                             |       -         3   |     -         -         -         -         -         -         -         -|       17        27        37        47        57        67        77      |  -         -  ||  | |-         -  |
                             2                 3   7                                                                            8                                                                          84              85| 87 |            90
                                                                                                                                                                                                                            86   89              

   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  (1, 1)

NMR Structure
Clan: SH3 (175)

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (VINEX_HUMAN | O60504)
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).
    GO:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0017166    vinculin binding    Interacting selectively and non-covalently with vinculin, a protein found in muscle, fibroblasts, and epithelial cells that binds actin and appears to mediate attachment of actin filaments to integral proteins of the plasma membrane.
biological process
    GO:0007015    actin filament organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0031589    cell-substrate adhesion    The attachment of a cell to the underlying substrate via adhesion molecules.
    GO:0006936    muscle contraction    A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:0051495    positive regulation of cytoskeleton organization    Any process that activates or increases the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0051496    positive regulation of stress fiber assembly    Any process that activates or increases the frequency, rate or extent of the assembly of a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.
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:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.


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 Related Entries

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

        VINEX_HUMAN | O605042ct3 2dlm 2nwm

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