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 HUMAN SHIP SH2 DOMAIN
 
Authors :  T. Kasai, S. Koshiba, S. Watanabe, T. Harada, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  04 Apr 07  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Sh2 Domain, Phosphotyrosine Binding Domain, Protein Tyrosine Kinase, Signal Transduction, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kasai, S. Koshiba, S. Watanabe, T. Harada, T. Kigawa, S. Yokoyama
Solution Structure Of The Human Ship Sh2 Domain
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIGNALING INOSITOL POLYPHOSPHATE PHOSPHATASE SHIP II
    Chains: A
    Engineered: YES
    Expression System Plasmid: P061218-23
    Expression System Vector Type: PLASMID
    Fragment: SH2 DOMAIN, UNP RESIDUES 1-112
    Gene: SHIP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS

 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 2YSX)

(-) Sites  (0, 0)

(no "Site" information available for 2YSX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.SHIP1_HUMAN5-101  1A:12-108

(-) Exons   (0, 0)

(no "Exon" information available for 2YSX)

(-) 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:119
 aligned with SHIP1_HUMAN | Q92835 from UniProtKB/Swiss-Prot  Length:1189

    Alignment length:119
                                   1                                                                                                               
                                   | 3        13        23        33        43        53        63        73        83        93       103         
          SHIP1_HUMAN     - -------MVPCWNHGNITRSKAEELLSRTGKDGSFLVRASESISRAYALCVLYRNCVYTYRILPNEDDKFTVQASEGVSMRFFTKLDQLIEFYKKENMGLVTHLQYPVPLEEEDTGDDP 112
               SCOP domains d2ysxa_ A: automated matches                                                                                            SCOP domains
               CATH domains 2ysxA00 A:1-119 SHC Adaptor Protein                                                                                     CATH domains
               Pfam domains -----------SH2-2ysxA01 A:12-93                                                               -------------------------- Pfam domains
         Sec.struct. author ............eee..hhhhhhhhhhhhh...eeeeee.......eeeeee....eeeeeeee.....eee............hhhhhhhhh............ee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------SH2  PDB: A:12-108 UniProt: 5-101                                                                ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2ysx A   1 GSSGSSGMVPCWNHGNITRSKAEELLSRTGKDGSFLVRASESISRAYALCVLYRNCVYTYRILPNEDDKFTVQASEGVSMRFFTKLDQLIEFYKKENMGLVTHLQYPVPLEEEDTGDDP 119
                                    10        20        30        40        50        60        70        80        90       100       110
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: SH2] (119)

(-) Gene Ontology  (42, 42)

NMR Structure(hide GO term definitions)
Chain A   (SHIP1_HUMAN | Q92835)
molecular function
    GO:0051425    PTB domain binding    Interacting selectively and non-covalently with a phosphotyrosine-binding (PTB) domain of a protein.
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0052659    inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity    Catalysis of the reaction: 1D-myo-inositol 1,3,4,5-tetrakisphosphate + H2O = 1D-myo-inositol 1,3,4-trisphosphate + phosphate.
    GO:0004445    inositol-polyphosphate 5-phosphatase activity    Catalysis of the reactions: D-myo-inositol 1,4,5-trisphosphate + H2O = myo-inositol 1,4-bisphosphate + phosphate, and 1D-myo-inositol 1,3,4,5-tetrakisphosphate + H2O = 1D-myo-inositol 1,3,4-trisphosphate + phosphate.
    GO:0034594    phosphatidylinositol trisphosphate phosphatase activity    Catalysis of the reaction: phosphatidylinositol trisphosphate + H2O = phosphatidylinositol bisphosphate + phosphate.
    GO:0016314    phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity    Catalysis of the reaction: phosphatidylinositol-3,4,5-trisphosphate + H2O = phosphatidylinositol-4,5-bisphosphate + phosphate.
    GO:0034485    phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity    Catalysis of the reaction: phosphatidylinositol-3,4,5-trisphosphate + H2O = phosphatidylinositol-3,4-bisphosphate + phosphate.
    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:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0008340    determination of adult lifespan    The control of viability and duration in the adult phase of the life-cycle.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0016064    immunoglobulin mediated immune response    An immune response mediated by immunoglobulins, whether cell-bound or in solution.
    GO:0043647    inositol phosphate metabolic process    The chemical reactions and pathways involving inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0050869    negative regulation of B cell activation    Any process that stops, prevents, or reduces the frequency, rate or extent of B cell activation.
    GO:0030889    negative regulation of B cell proliferation    Any process that stops, prevents or reduces the rate or extent of B cell proliferation.
    GO:0045779    negative regulation of bone resorption    Any process that stops, prevents, or reduces the frequency, rate or extent of bone resorption.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0030853    negative regulation of granulocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of granulocyte differentiation.
    GO:0050777    negative regulation of immune response    Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0045409    negative regulation of interleukin-6 biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-6.
    GO:0045656    negative regulation of monocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of monocyte differentiation.
    GO:0045659    negative regulation of neutrophil differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of neutrophil differentiation.
    GO:0045671    negative regulation of osteoclast differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of osteoclast differentiation.
    GO:0009968    negative regulation of signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
    GO:0006796    phosphate-containing compound metabolic process    The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
    GO:0006661    phosphatidylinositol biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid in which the sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0046856    phosphatidylinositol dephosphorylation    The process of removing one or more phosphate groups from a phosphatidylinositol.
    GO:0045579    positive regulation of B cell differentiation    Any process that activates or increases the frequency, rate or extent of B cell differentiation.
    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:0045648    positive regulation of erythrocyte differentiation    Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
    GO:0045621    positive regulation of lymphocyte differentiation    Any process that activates or increases the frequency, rate or extent of lymphocyte differentiation.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    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.

 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 2ysx)
 
  Sites
(no "Sites" information available for 2ysx)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ysx)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2ysx
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SHIP1_HUMAN | Q92835
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SHIP1_HUMAN | Q92835
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2YSX)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2YSX)