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(-) Description

Title :  THE FOURTH FN3 DOMAIN OF HUMAN SIDEKICK-2
 
Authors :  T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 May 04  (Deposition) - 07 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Sidekick-2, Fn3, Cell Adhesion, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Nagashima, F. Hayashi, S. Yokoyama
The Fourth Fn3 Domain Of Human Sidekick-2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIDEKICK 2
    ChainsA
    EngineeredYES
    Expression System PlasmidP040223-46
    Expression System Vector TypePLASMID
    FragmentFN3 DOMAIN
    GeneKAZUSA CDNA FH00815
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymDROSOPHILA SIDEKICK-LIKE, CHICKEN SIDEKICK 2-LIKE

 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 1WFN)

(-) Sites  (0, 0)

(no "Site" information available for 1WFN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.SDK2_HUMAN592-688
693-789
794-893
897-991
995-1094
1099-1197
1202-1299
1303-1397
1402-1499
1504-1621
1626-1722
1726-1821
1824-1923
  2-
-
-
A:20-113
A:116-119
-
-
-
-
-
-
-
-

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003926501ENSE00001774196chr17:71640227-7164016464SDK2_HUMAN1-22220--
1.2ENST000003926502ENSE00001512684chr17:71503736-71503577160SDK2_HUMAN22-75540--
1.3aENST000003926503aENSE00001512681chr17:71468357-71468251107SDK2_HUMAN75-111370--
1.4ENST000003926504ENSE00001512678chr17:71452192-71452045148SDK2_HUMAN111-160500--
1.5ENST000003926505ENSE00001512676chr17:71443887-71443754134SDK2_HUMAN160-205460--
1.6ENST000003926506ENSE00001512673chr17:71437062-71436951112SDK2_HUMAN205-242380--
1.7ENST000003926507ENSE00001421277chr17:71434293-71434103191SDK2_HUMAN242-306650--
1.8aENST000003926508aENSE00001197707chr17:71433961-7143387884SDK2_HUMAN306-334290--
1.9aENST000003926509aENSE00001325802chr17:71431783-71431589195SDK2_HUMAN334-399660--
1.10ENST0000039265010ENSE00001290139chr17:71429987-71429871117SDK2_HUMAN399-438400--
1.11ENST0000039265011ENSE00001310856chr17:71427808-71427641168SDK2_HUMAN438-494570--
1.12ENST0000039265012ENSE00001290905chr17:71426752-71426650103SDK2_HUMAN494-528350--
1.13ENST0000039265013ENSE00002158681chr17:71420231-71420055177SDK2_HUMAN528-587600--
1.14ENST0000039265014ENSE00001197681chr17:71419661-71419525137SDK2_HUMAN587-633470--
1.15ENST0000039265015ENSE00001326785chr17:71418573-71418426148SDK2_HUMAN633-682500--
1.16ENST0000039265016ENSE00001293900chr17:71415445-71415305141SDK2_HUMAN682-729480--
1.17ENST0000039265017ENSE00001327938chr17:71412131-71411950182SDK2_HUMAN729-790620--
1.18aENST0000039265018aENSE00001136771chr17:71410898-71410783116SDK2_HUMAN790-828390--
1.19ENST0000039265019ENSE00001340213chr17:71398280-71398085196SDK2_HUMAN829-894661A:1-1717
1.20ENST0000039265020ENSE00001293294chr17:71397891-7139779399SDK2_HUMAN894-927341A:17-5034
1.21ENST0000039265021ENSE00001330735chr17:71397350-71397159192SDK2_HUMAN927-991651A:50-11465
1.22ENST0000039265022ENSE00001797223chr17:71395428-71395307122SDK2_HUMAN991-1031411A:114-119 (gaps)10
1.23ENST0000039265023ENSE00001197653chr17:71394568-71394459110SDK2_HUMAN1032-1068370--
1.24ENST0000039265024ENSE00001328834chr17:71394324-71394174151SDK2_HUMAN1068-1118510--
1.25ENST0000039265025ENSE00001256056chr17:71391531-71391294238SDK2_HUMAN1119-1198800--
1.26ENST0000039265026ENSE00001256048chr17:71390463-71390348116SDK2_HUMAN1198-1236390--
1.27ENST0000039265027ENSE00001256039chr17:71389888-71389699190SDK2_HUMAN1237-1300640--
1.28ENST0000039265028ENSE00001256030chr17:71387677-7138757999SDK2_HUMAN1300-1333340--
1.29ENST0000039265029ENSE00001256022chr17:71386620-71386426195SDK2_HUMAN1333-1398660--
1.30ENST0000039265030ENSE00001256013chr17:71384176-71383975202SDK2_HUMAN1398-1465680--
1.31ENST0000039265031ENSE00001256005chr17:71382687-71382584104SDK2_HUMAN1465-1500360--
1.32ENST0000039265032ENSE00001255997chr17:71382056-7138198671SDK2_HUMAN1500-1523240--
1.33ENST0000039265033ENSE00001256344chr17:71380150-71380015136SDK2_HUMAN1524-1569460--
1.34ENST0000039265034ENSE00001255983chr17:71377089-7137703357SDK2_HUMAN1569-1588200--
1.35ENST0000039265035ENSE00001256243chr17:71375688-71375587102SDK2_HUMAN1588-1622350--
1.36ENST0000039265036ENSE00001256238chr17:71375431-71375316116SDK2_HUMAN1622-1660390--
1.38ENST0000039265038ENSE00001256232chr17:71364732-71364546187SDK2_HUMAN1661-1723630--
1.39ENST0000039265039ENSE00000947064chr17:71361534-71361397138SDK2_HUMAN1723-1769470--
1.40ENST0000039265040ENSE00000947066chr17:71357984-71357823162SDK2_HUMAN1769-1823550--
1.41aENST0000039265041aENSE00001300100chr17:71354343-71354218126SDK2_HUMAN1823-1865430--
1.42aENST0000039265042aENSE00000947069chr17:71348776-71348612165SDK2_HUMAN1865-1920560--
1.43aENST0000039265043aENSE00000947071chr17:71346929-71346789141SDK2_HUMAN1920-1967480--
1.44ENST0000039265044ENSE00000947072chr17:71346514-71346376139SDK2_HUMAN1967-2013470--
1.45ENST0000039265045ENSE00000947074chr17:71344864-71344738127SDK2_HUMAN2013-2055430--
1.46eENST0000039265046eENSE00001421304chr17:71335079-713305244556SDK2_HUMAN2056-21721170--

(-) 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:119
 aligned with SDK2_HUMAN | Q58EX2 from UniProtKB/Swiss-Prot  Length:2172

    Alignment length:123
                                   887       897       907       917       927       937       947       957       967       977       987       997   
          SDK2_HUMAN    878 GDGPRSTPQLVRTHEDVPGPVGHLSFSEILDTSLKVSWQEPGEKNGILTGYRISWEEYNRTNTRVTHYLPNVTLEYRVTGLTALTTYTIEVAAMTSKGQGQVSASTISSGVPPELPGPPTNLG 1000
               SCOP domains -------d1wfna1 A:8-113 Sidekick 2                                                                                ---------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------fn3-1wfnA01 A:19-103                                                                 -------------------- Pfam domains
         Sec.struct. author ........................eee.....eeeee............eeeeeeee..hhhhh..eee.....eeeee......eeeeeeeee....eeeeeeeeee......--....--. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE FN3  PDB: -     ---FN3  PDB: A:20-113 UniProt: 897-991                                                            ---FN3    PROSITE
           Transcript 1 (1) Exon 1.19        --------------------------------Exon 1.21  PDB: A:50-114 UniProt: 927-991                        --------- Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.20  PDB: A:17-50           ---------------------------------------------------------------Exon 1.22  Transcript 1 (2)
                1wfn A    1 GSSGSSGPQLVRTHEDVPGPVGHLSFSEILDTSLKVSWQEPGEKNGILTGYRISWEEYNRTNTRVTHYLPNVTLEYRVTGLTALTTYTIEVAAMTSKGQGQVSASTISSGVPPS--GPSS--G  119
                                    10        20        30        40        50        60        70        80        90       100       110   |  |118  |
                                                                                                                                           114  |  |  |
                                                                                                                                              115  |  |
                                                                                                                                                 118  |
                                                                                                                                                    119

   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 1WFN)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: E-set (290)

(-) Gene Ontology  (10, 10)

NMR Structure(hide GO term definitions)
Chain A   (SDK2_HUMAN | Q58EX2)
biological process
    GO:0060219    camera-type eye photoreceptor cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell in a camera-type eye.
    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: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:0010842    retina layer formation    The process in which the vertebrate retina is organized into three laminae: the outer nuclear layer (ONL), which contains photoreceptor nuclei; the inner nuclear layer (INL), which contains amacrine, bipolar and horizontal cells; and the retinal ganglion cell (RGC) layer. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells. The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells. Spanning all layers of the retina are the radially oriented Mueller glia.
    GO:0007416    synapse assembly    The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional).
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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        SDK2_HUMAN | Q58EX21wf5 1wfo 1wis

(-) Related Entries Specified in the PDB File

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