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(-) Description

Authors :  S. A. Dames, E. J. Bang, T. Ahrens, D. Haeussinger, S. Grzesiek
Date :  13 Jun 07  (Deposition) - 10 Jun 08  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Lipoprotein, Polymorphism, Glycoprotein, Cell Adhesion, Adiponectin Receptor, Extracellular Protein, Calcium, Membrane, T-Cadherin, Gpi-Anchor, Classical Cadherin, Cell-Cell Adhesion, Cleavage On Pair Of Basic Residues (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  S. A. Dames, E. J. Bang, D. Haeussinger, T. Ahrens, J. Engel, S. Grzesiek
Insights Into The Low Adhesive Capacity Of Human T- Cadherin From The Nmr Structure Of Its N-Terminal Extracellular Domain.
J. Biol. Chem. V. 283 23485 2008
PubMed-ID: 18550521  |  Reference-DOI: 10.1074/JBC.M708335200

(-) Compounds

Molecule 1 - CADHERIN-13
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET19B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Variant(DE3)
    Expression System Vector TypePLASMID
    FragmentEC1, RESIDUES 139-243
    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 2V37)

(-) Sites  (0, 0)

(no "Site" information available for 2V37)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V37)

(-) Cis Peptide Bonds  (4, 80)

NMR Structure
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Gln A:15 -Pro A:16
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Phe A:17 -Pro A:18
31, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Glu A:45 -Pro A:46
41, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Gly A:89 -Pro A:90

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V37)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
1CADHERIN_2PS50268 Cadherins domain profile.CAD13_HUMAN147-245
2CADHERIN_1PS00232 Cadherin domain signature.CAD13_HUMAN233-243

(-) Exons   (0, 0)

(no "Exon" information available for 2V37)

(-) 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 CAD13_HUMAN | P55290 from UniProtKB/Swiss-Prot  Length:713

    Alignment length:105
                                   148       158       168       178       188       198       208       218       228       238     
               SCOP domains d2v37a_ A: automated matches                                                                              SCOP domains
               CATH domains 2v37A00 A:1-105 Cadherins                                                                                 CATH domains
               Pfam domains ----Cadherin-2v37A01 A:5-98                                                                       ------- Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------CADHERIN_2  PDB: A:9-105 UniProt: 147-245                                                         PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------CADHERIN_1  PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                                    10        20        30        40        50        60        70        80        90       100     

   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: E-set (290)

(-) Gene Ontology  (43, 43)

NMR Structure(hide GO term definitions)
Chain A   (CAD13_HUMAN | P55290)
molecular function
    GO:0055100    adiponectin binding    Interacting selectively and non-covalently with adiponectin, a protein hormone produced by adipose tissue that modulates a number of metabolic processes, including glucose regulation and fatty acid catabolism.
    GO:0045296    cadherin binding    Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0071813    lipoprotein particle binding    Interacting selectively and non-covalently with a lipoprotein particle. A lipoprotein particle, also known as a lipoprotein, is a clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids.
    GO:0030169    low-density lipoprotein particle binding    Interacting selectively and non-covalently with a low-density lipoprotein particle, a lipoprotein particle that is rich in cholesterol esters and low in triglycerides, is typically composed of APOB100 and APOE, and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0016601    Rac protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Rac family of proteins switching to a GTP-bound active state.
    GO:0007266    Rho protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state.
    GO:0034332    adherens junction organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.
    GO:0016339    calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of one cell to another cell via adhesion molecules that require the presence of calcium for the interaction.
    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:0043542    endothelial cell migration    The orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:0007156    homophilic cell adhesion via plasma membrane adhesion molecules    The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell.
    GO:0043616    keratinocyte proliferation    The multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population. Keratinocytes are epidermal cells which synthesize keratin and undergo a characteristic change as they move upward from the basal layers of the epidermis to the cornified (horny) layer of the skin.
    GO:0030032    lamellipodium assembly    Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:0051668    localization within membrane    Any process in which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a membrane.
    GO:0055096    low-density lipoprotein particle mediated signaling    A series of molecular signals mediated by the detection of low-density lipoprotein particle.
    GO:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
    GO:0007162    negative regulation of cell adhesion    Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0050850    positive regulation of calcium-mediated signaling    Any process that activates or increases the frequency, rate or extent of calcium-mediated signaling.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0001954    positive regulation of cell-matrix adhesion    Any process that activates or increases the rate or extent of cell adhesion to an extracellular matrix.
    GO:0001938    positive regulation of endothelial cell proliferation    Any process that activates or increases the rate or extent of endothelial cell proliferation.
    GO:0050927    positive regulation of positive chemotaxis    Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
    GO:0048661    positive regulation of smooth muscle cell proliferation    Any process that activates or increases the rate or extent of smooth muscle cell proliferation.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0030100    regulation of endocytosis    Any process that modulates the frequency, rate or extent of endocytosis.
    GO:0042058    regulation of epidermal growth factor receptor signaling pathway    Any process that modulates the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:0010033    response to organic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
    GO:0002040    sprouting angiogenesis    The extension of new blood vessels from existing capillaries into avascular tissues resulting from the proliferation of blood vessel endothelial cells.
cellular component
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0005901    caveola    A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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: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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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.


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    Gln A:15 - Pro A:16   [ RasMol ]  
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