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(-) Description

Title :  STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR DISULFIDE BOND HETEROGENEITY IN ACTIVE FORMS OF THE SOMATOMEDIN B DOMAIN OF HUMAN VITRONECTIN
 
Authors :  Y. Kamikubo, R. De Guzman, G. Kroon, S. Curriden, J. G. Neels, M. J. Churchill, P. Dawson, S. Oldziej, A. Jagielska, H. A. Scheraga, D. J. Loskutoff, H. J. Dyson
Date :  24 Mar 04  (Deposition) - 27 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Somatostatin B Domain, Vitronectin, Nmr Structure, Disulfide Bonds Heterogeneity, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kamikubo, R. De Guzman, G. Kroon, S. Curriden, J. G. Neels, M. J. Churchill, P. Dawson, S. Oldziej, A. Jagielska, H. A. Scheraga, D. J. Loskutoff, H. J. Dyson
Disulfide Bonding Arrangements In Active Forms Of The Somatomedin B Domain Of Human Vitronectin.
Biochemistry V. 43 6519 2004
PubMed-ID: 15157085  |  Reference-DOI: 10.1021/BI049647C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VITRONECTIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-32A
    Expression System StrainBL21TRXB(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSOMATOMEDIN B DOMAIN OF HUMAN VITRONECTIN
    GeneVTN
    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 1SSU)

(-) Sites  (0, 0)

(no "Site" information available for 1SSU)

(-) SS Bonds  (4, 4)

NMR Structure
No.Residues
1A:5 -A:9
2A:19 -A:21
3A:25 -A:31
4A:32 -A:39

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMB_2PS50958 Somatomedin B (SMB) domain profile.VTNC_HUMAN20-63  1A:1-44
2SMB_1PS00524 Somatomedin B domain (SMB) signature.VTNC_HUMAN38-58  1A:19-39

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002262181ENSE00001177296chr17:26697717-26697161557VTNC_HUMAN1-22221A:1-33
1.2ENST000002262182ENSE00000705689chr17:26697067-26696948120VTNC_HUMAN22-62411A:3-4341
1.3ENST000002262183ENSE00000866275chr17:26696872-26696528345VTNC_HUMAN62-1771161A:43-519
1.4ENST000002262184ENSE00000866274chr17:26696449-26696310140VTNC_HUMAN177-223470--
1.5ENST000002262185ENSE00000705693chr17:26696049-26695893157VTNC_HUMAN224-276530--
1.6ENST000002262186ENSE00000705695chr17:26695694-26695542153VTNC_HUMAN276-327520--
1.7aENST000002262187aENSE00000705697chr17:26695080-26694736345VTNC_HUMAN327-4421160--
1.8bENST000002262188bENSE00001177290chr17:26694502-26694297206VTNC_HUMAN442-478370--

(-) 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:51
 aligned with VTNC_HUMAN | P04004 from UniProtKB/Swiss-Prot  Length:478

    Alignment length:51
                                    29        39        49        59        69 
            VTNC_HUMAN   20 DQESCKGRCTEGFNVDKKCQCDELCSYYQSCCTDYTAECKPQVTRGDVFTM 70
               SCOP domains d1ssua_ A: Vitronectin                              SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains Somatomedin_B-1ssuA01 A:1-44                ------- Pfam domains
         Sec.struct. author .......................hhhhh.....hhhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                PROSITE (1) SMB_2  PDB: A:1-44 UniProt: 20-63           ------- PROSITE (1)
                PROSITE (2) ------------------SMB_1  PDB: A:19-39  ------------ PROSITE (2)
           Transcript 1 (1) 1.1---------------------------------------Exon 1.3  Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: A:3-43 UniProt: 22-62     -------- Transcript 1 (2)
                  1ssu A  1 DQESCKGRCTEGFNVDKKCQCDELCSYYQSCCTDYTAECKPQVTRGDVFTM 51
                                    10        20        30        40        50 

   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 1SSU)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (32, 32)

NMR Structure(hide GO term definitions)
Chain A   (VTNC_HUMAN | P04004)
molecular function
    GO:0050840    extracellular matrix binding    Interacting selectively and non-covalently with a component of the extracellular matrix.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0030247    polysaccharide binding    Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    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:0005044    scavenger receptor activity    Combining with any modified low-density lipoprotein (LDL) or other polyanionic ligand and delivering the ligand into the cell via endocytosis. Ligands include acetylated and oxidized LDL, Gram-positive and Gram-negative bacteria, apoptotic cells, amyloid-beta fibrils, and advanced glycation end products (AGEs).
biological process
    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:0033627    cell adhesion mediated by integrin    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits.
    GO:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0035987    endodermal cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0030195    negative regulation of blood coagulation    Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0048709    oligodendrocyte differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system.
    GO:0010811    positive regulation of cell-substrate adhesion    Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:0048260    positive regulation of receptor-mediated endocytosis    Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    GO:0014911    positive regulation of smooth muscle cell migration    Any process that activates, maintains or increases the frequency, rate or extent of smooth muscle cell migration.
    GO:0030949    positive regulation of vascular endothelial growth factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
    GO:0090303    positive regulation of wound healing    Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0030449    regulation of complement activation    Any process that modulates the frequency, rate or extent of complement activation.
    GO:0061302    smooth muscle cell-matrix adhesion    The binding of a smooth muscle cell to the extracellular matrix via adhesion molecules.
cellular component
    GO:0071062    alphav-beta3 integrin-vitronectin complex    A protein complex that consists of an alphav-beta3 integrin complex bound to vitronectin.
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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 Related Entries

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

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        VTNC_HUMAN | P040041oc0 1s4g 2jq8 3bt1 3bt2 4k24

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