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(-) Description

Title :  SOLUTION STRUCTURE OF THE SECOND FNIII DOMAIN OF DSCAML1 PROTEIN
 
Authors :  X. -R. Qin, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  13 Feb 04  (Deposition) - 22 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Fniii Domain, Dscaml1 Protein, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. -R. Qin, F. Hayashi, S. Yokoyama
Solution Structure Of The Second Fniii Domain Of Dscaml1 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DOWN SYNDROME CELL ADHESION MOLECULE LIKE- PROTEIN 1B
    ChainsA
    EngineeredYES
    Expression System PlasmidP030623-12
    Expression System Vector TypePLASMID
    FragmentFNIII DOMAIN
    GeneKAZUSA CDNA KIAA1132
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS

 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 1VA9)

(-) Sites  (0, 0)

(no "Site" information available for 1VA9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VA9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VA9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VA9)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.DSCL1_HUMAN887-984
989-1088
1093-1189
1193-1288
1383-1477
1478-1578
  2-
A:18-116
A:122-122
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1VA9)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:122
 aligned with DSCL1_HUMAN | Q8TD84 from UniProtKB/Swiss-Prot  Length:2053

    Alignment length:153
                                   978       988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118   
         DSCL1_HUMAN    969 GRSEPSKELTISTEEAAPDGPPMDVTLQPVTSQSIQVTWKAPKKELQNGVIRGYQIGYRENSPGSNGQYSIVEMKATGDSEVYTLDNLKKFAQYGVVVQAFNRAGTGPSSSEINATTLEDVPSQPPENVRALSITSDVAVISWSEPPRSTLNG 1121
               SCOP domains ----------d1va9a1 A:8-116 Down syndrome cell adhesion molecule-like protein 1, DSCAML1                                 ---------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------fn3-1va9A01 A:17-107                                                                       ------------------------------------------- Pfam domains
         Sec.struct. author .......---............eeeeeee....eeeeeee............eeeeeeee...................eeeeeee.......eeeeeeeee..ee......ee.........----------------------------.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE FN3  PDB: -     ----FN3  PDB: A:18-116 UniProt: 989-1088                                                                ----FN3  PDB: A:122-122           PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1va9 A    1 GSSGSSG---ISTEEAAPDGPPMDVTLQPVTSQSIQVTWKAPKKELQNGVIRGYQIGYRENSPGSNGQYSIVEMKATGDSEVYTLDNLKKFAQYGVVVQAFNRAGTGPSSSEINATTLESGPS----------------------------SG  122
                                  |  -|       17        27        37        47        57        67        77        87        97       107       117  |      -         -         - | 
                                  7   8                                                                                                             120                          121 

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    → 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 1VA9)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: E-set (290)

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (DSCL1_HUMAN | Q8TD84)
molecular function
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0007409    axonogenesis    De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    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:0001709    cell fate determination    A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0009953    dorsal/ventral pattern formation    The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
    GO:0048704    embryonic skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized during the embryonic phase.
    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:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
cellular component
    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: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: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: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.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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