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(-) Description

Title :  HYALURONAN-BINDING DOMAIN OF CD44 IN ITS LIGAND-BOUND FORM
 
Authors :  M. Takeda, S. Ogino, R. Umemoto, M. Sakakura, M. Kajiwara, K. N. Sugahara, H. Hayasaka, M. Miyasaka, H. Terasawa, I. Shimada
Date :  01 Sep 06  (Deposition) - 21 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Link Module, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Takeda, S. Ogino, R. Umemoto, M. Sakakura, M. Kajiwara, K. N. Sugahara, H. Hayasaka, M. Miyasaka, H. Terasawa, I. Shimada
Ligand-Induced Structural Changes Of The Cd44 Hyaluronan-Binding Domain Revealed By Nmr
J. Biol. Chem. V. 281 40089 2006
PubMed-ID: 17085435  |  Reference-DOI: 10.1074/JBC.M608425200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CD44 ANTIGEN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET11
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentHYALURONAN BINDING DOMAIN RESIDUE 21-178
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPHAGOCYTIC GLYCOPROTEIN I, PGP-1, HUTCH-I, EXTRACELLULAR MATRIX RECEPTOR-III, ECMR-III, GP90 LYMPHOCYTE HOMING/ADHESION RECEPTOR, HERMES ANTIGEN, HYALURONATE RECEPTOR, HEPARAN SULFATE PROTEOGLYCAN, EPICAN, CDW44

 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 2I83)

(-) Sites  (0, 0)

(no "Site" information available for 2I83)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:28 -A:129
2A:53 -A:118
3A:77 -A:97

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I83)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_006490R46PCD44_HUMANPolymorphism369473842AR46P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LINK_2PS50963 Link domain profile.CD44_HUMAN32-120  1A:32-120
2LINK_1PS01241 Link domain signature.CD44_HUMAN53-97  1A:53-97

(-) Exons   (0, 0)

(no "Exon" information available for 2I83)

(-) 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:158
 aligned with CD44_HUMAN | P16070 from UniProtKB/Swiss-Prot  Length:742

    Alignment length:158
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
           CD44_HUMAN    21 QIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDV 178
               SCOP domains d2i83a_ A: CD44, hyaluronan binding domain                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeeee......hhhhhhhhhhh......hhhhhhhhh................eeee......hhhhh.eeee.........eeee.......................eeeee............................... Sec.struct. author
                 SAPs(SNPs) -------------------------P------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------LINK_2  PDB: A:32-120 UniProt: 32-120                                                    ---------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------LINK_1  PDB: A:53-97 UniProt: 53-97          --------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i83 A  21 QIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDV 178
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        

   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 2I83)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I83)

(-) Gene Ontology  (35, 35)

NMR Structure(hide GO term definitions)
Chain A   (CD44_HUMAN | P16070)
molecular function
    GO:0005518    collagen binding    Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
    GO:0004896    cytokine receptor activity    Combining with a cytokine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0005540    hyaluronic acid binding    Interacting selectively and non-covalently with hyaluronic acid, a polymer composed of repeating dimeric units of glucuronic acid and N-acetyl glucosamine.
    GO:0004415    hyalurononglucosaminidase activity    Catalysis of the random hydrolysis of (1->4) linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate.
    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:0051216    cartilage development    The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    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:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0044344    cellular response to fibroblast growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an fibroblast growth factor stimulus.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    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:0030214    hyaluronan catabolic process    The chemical reactions and pathways resulting in the breakdown of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
    GO:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0070487    monocyte aggregation    The adhesion of one monocyte to one or more other monocytes via adhesion molecules.
    GO:0043518    negative regulation of DNA damage response, signal transduction by p53 class mediator    Any process that stops, prevents, or reduces the frequency, rate or extent of the cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:1902166    negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator    Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0034116    positive regulation of heterotypic cell-cell adhesion    Any process that activates or increases the frequency, rate, or extent of heterotypic cell-cell adhesion.
    GO:1900625    positive regulation of monocyte aggregation    Any process that activates or increases the frequency, rate or extent of monocyte aggregation.
    GO:0033138    positive regulation of peptidyl-serine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    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:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0035692    macrophage migration inhibitory factor receptor complex    A protein complex that binds macrophage migration inhibitory factor. Comprises CD74 and CD44 cell surface proteins.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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 Related Entries

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

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        CD44_HUMAN | P160701poz 1uuh 4pz3 4pz4

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