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(-) Description

Title :  SOLUTION STRUCTURES OF THE SH2 DOMAIN OF HUMAN PROTEIN-TYROSINE PHOSPHATASE SHP-1
 
Authors :  M. Sato, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  17 May 05  (Deposition) - 17 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Sh2 Domain, Hcp, Ptp1C, 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 :  M. Sato, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structures Of The Sh2 Domain Of Human Protein-Tyrosine Phosphatase Shp-1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE, NON-RECEPTOR TYPE 6
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression System PlasmidP040607-04
    Expression System Vector TypePLASMID
    FragmentSH2 DOMAIN
    GenePTPN6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymPROTEIN-TYROSINE PHOSPHATASE 1C, PTP-1C, HEMATOPOIETIC CELL PROTEIN-TYROSINE PHOSPHATASE, SH-PTP1, PROTEIN-TYROSINE PHOSPHATASE SHP-1

 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 1X6C)

(-) Sites  (0, 0)

(no "Site" information available for 1X6C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X6C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X6C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X6C)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.PTN6_HUMAN4-100
110-213
  1-
A:8-111
2TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTN6_HUMAN244-515  1A:114-118

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3ENST000003189743ENSE00001164365chr12:7060434-7060683250PTN6_HUMAN1-330--
1.4ENST000003189744ENSE00000866991chr12:7060772-7060894123PTN6_HUMAN3-44420--
1.5ENST000003189745ENSE00000716206chr12:7061146-7061340195PTN6_HUMAN44-109661A:1-7 (gaps)55
1.6ENST000003189746ENSE00000716209chr12:7063968-7064157190PTN6_HUMAN109-172641A:7-7064
1.7ENST000003189747ENSE00000716212chr12:7064314-7064430117PTN6_HUMAN173-211391A:71-10939
1.8ENST000003189748ENSE00000716214chr12:7064535-7064648114PTN6_HUMAN212-249381A:110-1134
1.9ENST000003189749ENSE00000716216chr12:7064823-706491997PTN6_HUMAN250-282330--
1.10ENST0000031897410ENSE00000716218chr12:7065305-706538480PTN6_HUMAN282-308270--
1.11ENST0000031897411ENSE00000716220chr12:7065582-7065731150PTN6_HUMAN309-358501A:114-118 (gaps)14
1.12ENST0000031897412ENSE00000716222chr12:7066817-7066948132PTN6_HUMAN359-402440--
1.13ENST0000031897413ENSE00000716225chr12:7067082-7067236155PTN6_HUMAN403-454520--
1.14ENST0000031897414ENSE00000716227chr12:7069090-706915768PTN6_HUMAN454-477240--
1.15ENST0000031897415ENSE00000716229chr12:7069251-7069402152PTN6_HUMAN477-527510--
1.16ENST0000031897416ENSE00000716231chr12:7069507-706959892PTN6_HUMAN528-558310--
1.17cENST0000031897417cENSE00001358823chr12:7069969-7070108140PTN6_HUMAN558-595380--
1.18ENST0000031897418ENSE00001365384chr12:7070289-7070479191PTN6_HUMAN-00--

(-) 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:118
 aligned with PTN6_HUMAN | P29350 from UniProtKB/Swiss-Prot  Length:595

    Alignment length:272
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324  
           PTN6_HUMAN    55 QNSGDFYDLYGGEKFATLTELVEYYTQQQGVLQDRDGTIIHLKYPLNCSDPTSERWYHGHMSGGQAETLLQAKGEPWTFLVRESLSQPGDFVLSVLSDQPKAGPGSPLRVTHIKVMCEGGRYTVGGLETFDSLTDLVEHFKKTGIEEASGAFVYLRQPYYATRVNAADIENRVLELNKKQESEDTAKAGFWEEFESLQKQEVKNLHQRLEGQRPENKGKNRYKNILPFDHSRVILQGRDSNIPGSDYINANYIKNQLLGPDENAKTYIASQG 326
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1x6c                                                A00 A:1-118 SHC Adaptor Protein                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....------------------------------------------------.........hhhhhhhhhhhhh...eeeeee.......eeeeeeeeee.......eeeeeeeeeee..eee........hhhhhhhhhhhhhee.....ee...ee...-------------------------------------------------------------------------------------------------..---------... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE SH2  PDB: - UniProt: 4-100                    ---------SH2  PDB: A:8-111 UniProt: 110-213                                                                      ------------------------------TYR_PHOSPHATASE_PTP  PDB: A:114-118 UniProt: 244-515                                PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:1-7 (gaps) UniProt: 44-109            ---------------------------------------------------------------Exon 1.7  PDB: A:71-109                Exon 1.8  PDB: A:110-113 [INCOMPLETE] --------------------------------Exon 1.10  PDB: -          Exon 1.11          Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.6  PDB: A:7-70 UniProt: 109-172                          -----------------------------------------------------------------------------Exon 1.9  PDB: - UniProt: 250-282-------------------------------------------- Transcript 1 (2)
                 1x6c A   1 GSSG------------------------------------------------SSGWYHGHMSGGQAETLLQAKGEPWTFLVRESLSQPGDFVLSVLSDQPKAGPGSPLRVTHIKVMCEGGRYTVGGLETFDSLTDLVEHFKKTGIEEASGAFVYLRQPYYS-------------------------------------------------------------------------------------------------GP---------SSG 118
                               |     -         -         -         -         -  |     12        22        32        42        52        62        72        82        92       102       112|        -         -         -         -         -         -         -         -         -       115       116  
                               4                                                5                                                                                                         113                                                                                               114|       116  
                                                                                                                                                                                                                                                                                             115            

   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  (0, 0)

(no "SCOP Domain" information available for 1X6C)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1X6C)

(-) Gene Ontology  (53, 53)

NMR Structure(hide GO term definitions)
Chain A   (PTN6_HUMAN | P29350)
molecular function
    GO:0042169    SH2 domain binding    Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.
    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:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    GO:0001784    phosphotyrosine residue binding    Interacting selectively and non-covalently with a phosphorylated tyrosine residue within a protein.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0005001    transmembrane receptor protein tyrosine phosphatase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0050853    B cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0033277    abortive mitotic cell cycle    A cell cycle in which mitosis is begun and progresses normally through the end of anaphase, but not completed, resulting in a cell with increased ploidy.
    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: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:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0002244    hematopoietic progenitor cell differentiation    The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
    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:0035855    megakaryocyte development    The process whose specific outcome is the progression of a megakaryocyte cell over time, from its formation to the mature structure. Megakaryocyte development does not include the steps involved in committing a cell to a megakaryocyte fate. A megakaryocyte is a giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow.
    GO:0042267    natural killer cell mediated cytotoxicity    The directed killing of a target cell by a natural killer cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
    GO:0050859    negative regulation of B cell receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0043407    negative regulation of MAP kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity.
    GO:0043409    negative regulation of MAPK cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the MAPKKK cascade.
    GO:0042130    negative regulation of T cell proliferation    Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
    GO:0050860    negative regulation of T cell receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0002924    negative regulation of humoral immune response mediated by circulating immunoglobulin    Any process that stops, prevents, or reduces the frequency, rate, or extent of a humoral immune response mediated by circulating immunoglobulin.
    GO:0050732    negative regulation of peptidyl-tyrosine phosphorylation    Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0070527    platelet aggregation    The adhesion of one platelet to one or more other platelets via adhesion molecules.
    GO:0030220    platelet formation    The process in which platelets bud from long processes extended by megakaryocytes.
    GO:0033630    positive regulation of cell adhesion mediated by integrin    Any process that activates or increases the frequency, rate, or extent of cell adhesion mediated by integrin.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0045577    regulation of B cell differentiation    Any process that modulates the frequency, rate or extent of B cell differentiation.
    GO:0070372    regulation of ERK1 and ERK2 cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:2000045    regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that controls the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:0051279    regulation of release of sequestered calcium ion into cytosol    Any process that modulates the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
    GO:0060338    regulation of type I interferon-mediated signaling pathway    Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
cellular component
    GO:0042105    alpha-beta T cell receptor complex    A T cell receptor complex in which the TCR heterodimer comprises alpha and beta chains, associated with the CD3 complex; recognizes a complex consisting of an antigen-derived peptide bound to a class I or class II MHC protein.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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

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        PTN6_HUMAN | P293501fpr 1gwz 2b3o 2rmx 2yu7 3ps5 4gry 4grz 4gs0 4hjp 4hjq

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