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(-) Description

Title :  SOLUTION STRUCTURE OF THE FIRST CADHERIN DOMAIN FROM HUMAN DESMOGLEIN-2
 
Authors :  R. Sano, F. Hayashi, M. Yoshida, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Cadherin, Hdgc, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Sano, F. Hayashi, M. Yoshida, S. Yokoyama
Solution Structure Of The First Cadherin Domain From Human Desmoglein-2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DESMOGLEIN-2
    ChainsA
    EngineeredYES
    Expression System PlasmidP060522-08
    Expression System Vector TypePLASMID
    FragmentCADHERIN, UNP RESIDUES 47-162
    GeneDSG2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymHDGC

 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 2YQG)

(-) Sites  (0, 0)

(no "Site" information available for 2YQG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 40)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Asn A:29 -Pro A:30
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Pro A:58 -Pro A:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

NMR Structure (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_029366R49HDSG2_HUMANDisease (ARVD10)121913006AR10H
2UniProtVAR_062387V56MDSG2_HUMANPolymorphism121913013AV17M
3UniProtVAR_048508Y89CDSG2_HUMANPolymorphism2230232AY50C
4UniProtVAR_062388V158GDSG2_HUMANPolymorphism191143292AV119G

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

(-) PROSITE Motifs  (2, 3)

NMR Structure (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CADHERIN_2PS50268 Cadherins domain profile.DSG2_HUMAN70-159
160-272
282-393
392-499
  2A:31-120
A:121-123
-
-
2CADHERIN_1PS00232 Cadherin domain signature.DSG2_HUMAN147-157
260-270
487-497
  1A:108-118
-
-

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002615901ENSE00001401353chr18:29078027-29078259233DSG2_HUMAN1-15151A:1-44
1.2ENST000002615902ENSE00001107952chr18:29098202-2909823736DSG2_HUMAN16-27121A:5-73
1.3ENST000002615903ENSE00001107966chr18:29099766-29099900135DSG2_HUMAN28-72451A:8-3326
1.4ENST000002615904ENSE00001107958chr18:29100766-29100927162DSG2_HUMAN73-126541A:34-8754
1.5ENST000002615905ENSE00001107970chr18:29101062-29101206145DSG2_HUMAN127-175491A:88-12336
1.6ENST000002615906ENSE00001107964chr18:29102046-29102212167DSG2_HUMAN175-230560--
1.7ENST000002615907ENSE00001107968chr18:29104411-29104548138DSG2_HUMAN231-276460--
1.8ENST000002615908ENSE00001107962chr18:29104666-29104851186DSG2_HUMAN277-338620--
1.9ENST000002615909ENSE00000998595chr18:29110950-29111215266DSG2_HUMAN339-427890--
1.10ENST0000026159010ENSE00000796930chr18:29115233-29115375143DSG2_HUMAN427-475490--
1.11ENST0000026159011ENSE00000796931chr18:29116165-29116392228DSG2_HUMAN475-551770--
1.12ENST0000026159012ENSE00000796932chr18:29118714-29118941228DSG2_HUMAN551-627770--
1.13ENST0000026159013ENSE00000796933chr18:29121156-29121277122DSG2_HUMAN627-667410--
1.14ENST0000026159014ENSE00000796934chr18:29122483-29122815333DSG2_HUMAN668-7781110--
1.15ENST0000026159015ENSE00000796935chr18:29125684-291288133130DSG2_HUMAN779-11183400--

(-) 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:123
 aligned with DSG2_HUMAN | Q14126 from UniProtKB/Swiss-Prot  Length:1118

    Alignment length:160
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162
           DSG2_HUMAN     3 RSPGRAYALLLLLICFNVGSGLHLQVLSTRNENKLLPKHPHLVRQKRAWITAPVALREGEDLSKKNPIAKIHSDLAEERGLKITYKYTGKGITEPPFGIFVFNKDTGELNVTSILDREETPFFLLTGYALDARGNNVEKPLELRIKVLDINDNEPVFTQD 162
               SCOP domains d2yq              ga_                        A: automated matches                                                                                                SCOP domains
               CATH domains 2yqg              A00                        A:1-123 Cadherins                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....--------------...-----------------------.........eeee................hhhhhhh...eeeeee..........eeee....eeee..........eeeeeeeee.....eeeeee..eeeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------H------M--------------------------------C--------------------------------------------------------------------G---- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------CADHERIN_2  PDB: A:31-120 UniProt: 70-159                                                 CAD PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------CADHERIN_1 ----- PROSITE (2)
               Transcript 1 Exon 1.1     Exon 1.2    Exon 1.3  PDB: A:8-33 UniProt: 28-72         Exon 1.4  PDB: A:34-87 UniProt: 73-126                Exon 1.5  PDB: A:88-123 [INCOMPLETE] Transcript 1
                 2yqg A   1 GSSG--------------SSG-----------------------QKRAWITAPVALREGEDLSKKNPIAKIHSDLAEERGLKITYKYTGKGITEPPFGIFVFNKDTGELNVTSILDREETPFFLLTGYALDARGNNVEKPLELRIKVLDINDNEPVFTQD 123
                               |     -        |6|        -         -    |   13        23        33        43        53        63        73        83        93       103       113       123
                               4              5 7                       8                                                                                                                   

   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  (0, 0)

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

(-) Gene Ontology  (24, 24)

NMR Structure(hide GO term definitions)
Chain A   (DSG2_HUMAN | Q14126)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0086083    cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication    Interacting selectively and non-covalently with any protein or protein complex that results in the connection of a bundle of His cell with a Purkinje myocyte and contributes to the communication between the two cells.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0003165    Purkinje myocyte development    The process whose specific outcome is the progression of a Purkinje myocyte over time, from its formation to the mature structure. The Purkinje myocyte (also known as cardiac Purkinje fiber) is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle.
    GO:0086073    bundle of His cell-Purkinje myocyte adhesion involved in cell communication    The attachment of a bundle of His cell to a Purkinje myocyte via adhesion molecules that results in the cells being juxtaposed so that they can communicate.
    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:0002934    desmosome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a desmosome. A desmosome is a patch-like intercellular junction found in vertebrate tissues, consisting of parallel zones of two cell membranes, separated by an space of 25-35 nm, and having dense fibrillar plaques in the subjacent cytoplasm.
    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:0060135    maternal process involved in female pregnancy    A reproductive process occurring in the mother that allows an embryo or fetus to develop within it.
    GO:0086091    regulation of heart rate by cardiac conduction    A cardiac conduction process that modulates the frequency or rate of heart contraction.
    GO:0098911    regulation of ventricular cardiac muscle cell action potential    Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a ventricular cardiac muscle cell contributing to the regulation of its contraction. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
    GO:0032570    response to progesterone    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 a progesterone stimulus.
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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:0030057    desmosome    A cell-cell junction in which: on the cytoplasmic surface of each interacting plasma membrane is a dense plaque composed of a mixture of intracellular anchor proteins; a bundle of keratin intermediate filaments is attached to the surface of each plaque; transmembrane adhesion proteins of the cadherin family bind to the plaques and interact through their extracellular domains to hold the adjacent membranes together by a Ca2+-dependent mechanism.
    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: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:0014704    intercalated disc    A complex cell-cell junction at which myofibrils terminate in cardiomyocytes; mediates mechanical and electrochemical integration between individual cardiomyocytes. The intercalated disc contains regions of tight mechanical attachment (fasciae adherentes and desmosomes) and electrical coupling (gap junctions) between adjacent cells.
    GO:0016328    lateral plasma membrane    The portion of the plasma membrane at the lateral side of the cell. In epithelial cells, lateral plasma membranes are on the sides of cells which lie at the interface of adjacent cells.
    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

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        DSG2_HUMAN | Q141265erd 5j5j

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