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(-) Description

Title :  THE SOLUTION STRUCTURE OF THE FOURTH FIBRONECTIN TYPE III DOMAIN OF HUMAN NEOGENIN
 
Authors :  N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 May 05  (Deposition) - 15 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rgm Binding, Fibronectin Type Iii Domain, 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 :  N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
The Solution Structure Of The Fourth Fibronectin Type Iii Domain Of Human Neogenin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEOGENIN
    ChainsA
    EngineeredYES
    Expression System PlasmidP041213-05
    Expression System Vector TypePLASMID
    FragmentFN3 DOMAIN
    GeneNEO1
    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 1X5I)

(-) Sites  (0, 0)

(no "Site" information available for 1X5I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X5I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X5I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X5I)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.NEO1_HUMAN441-535
541-631
636-731
741-831
856-952
957-1054
  2-
-
-
A:30-120
A:123-126
-

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003393621ENSE00002172289chr15:73344875-73345146272NEO1_HUMAN1-44440--
1.2ENST000003393622ENSE00001675359chr15:73408881-73409198318NEO1_HUMAN44-1501070--
1.3ENST000003393623ENSE00001769067chr15:73414866-73415141276NEO1_HUMAN150-242930--
1.4ENST000003393624ENSE00001670832chr15:73418758-73418911154NEO1_HUMAN242-293520--
1.5ENST000003393625ENSE00000697549chr15:73428232-73428368137NEO1_HUMAN293-339470--
1.6ENST000003393626ENSE00001210876chr15:73468744-73468898155NEO1_HUMAN339-390520--
1.7ENST000003393627ENSE00001210873chr15:73470648-73470768121NEO1_HUMAN391-431410--
1.8bENST000003393628bENSE00001210869chr15:73528688-73528847160NEO1_HUMAN431-484540--
1.9ENST000003393629ENSE00001110167chr15:73536685-73536839155NEO1_HUMAN484-536530--
1.10ENST0000033936210ENSE00000943178chr15:73541401-73541549149NEO1_HUMAN536-585500--
1.11ENST0000033936211ENSE00000943179chr15:73541924-73542062139NEO1_HUMAN586-632470--
1.12ENST0000033936212ENSE00000943180chr15:73545741-7354579050NEO1_HUMAN632-648170--
1.13ENST0000033936213ENSE00000943181chr15:73547023-73547170148NEO1_HUMAN649-698501A:1-5 (gaps)15
1.14ENST0000033936214ENSE00000943182chr15:73551107-73551217111NEO1_HUMAN698-735381A:6-2419
1.15ENST0000033936215ENSE00000943183chr15:73552612-73552806195NEO1_HUMAN735-800661A:24-8966
1.16ENST0000033936216ENSE00000943184chr15:73558657-7355875296NEO1_HUMAN800-832331A:89-12133
1.17aENST0000033936217aENSE00001164418chr15:73562351-73562574224NEO1_HUMAN832-906751A:121-126 (gaps)28
1.18ENST0000033936218ENSE00001164373chr15:73562657-73562795139NEO1_HUMAN907-953470--
1.19ENST0000033936219ENSE00001110147chr15:73564796-73564903108NEO1_HUMAN953-989370--
1.20ENST0000033936220ENSE00001322047chr15:73566152-73566346195NEO1_HUMAN989-1054660--
1.21ENST0000033936221ENSE00001210834chr15:73567033-7356706533NEO1_HUMAN1054-1065120--
1.22ENST0000033936222ENSE00001210830chr15:73570472-7357054069NEO1_HUMAN1065-1088240--
1.23ENST0000033936223ENSE00000885623chr15:73575305-73575452148NEO1_HUMAN1088-1137500--
1.24ENST0000033936224ENSE00001319812chr15:73580654-73580892239NEO1_HUMAN1137-1217810--
1.25ENST0000033936225ENSE00000373859chr15:73581487-7358157993NEO1_HUMAN1217-1248320--
1.27ENST0000033936227ENSE00000697751chr15:73590689-73590952264NEO1_HUMAN1248-1336890--
1.28ENST0000033936228ENSE00000697755chr15:73593662-73593798137NEO1_HUMAN1336-1381460--
1.29aENST0000033936229aENSE00001389723chr15:73594954-735975432590NEO1_HUMAN1382-1408270--

(-) 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:126
 aligned with NEO1_HUMAN | Q92859 from UniProtKB/Swiss-Prot  Length:1461

    Alignment length:184
                                   685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855    
           NEO1_HUMAN   676 ASRKSDVTETLVSGTQLSQLIEGLDRGTEYNFRVAALTINGTGPATDWLSAETFESDLDETRVPEVPSSLHVRPLVTSIVVSWTPPENQNIVVRGYAIGYGIGSPHAQTIKVDYKQRYYTIENLDPSSHYVITLKAFNNVGEGIPLYESAVTRPHTDTSEVDLFVINAPYTPVPDPTPMMPPVG 859
               SCOP domains -------------------------------------------d1x5ia1 A:8-120 Neogenin                                                                                         ---------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------fn3-1x5iA01 A:29-109                                                             --------------------------------------- Pfam domains
         Sec.struct. author ..----------...--------------------------...........................eeeeeee..eeeeeee..........eeeeee...hhhheeee......eeee.......ee..eeeee............ee.......----------------------.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE FN3  PDB: - UniProt: 636-731                            ---------FN3  PDB: A:30-120 UniProt: 741-831                                                        ------------------------FN3  PROSITE
           Transcript 1 (1) Exon 1.13 [INCOMPLETE] ------------------------------------Exon 1.15  PDB: A:24-89 UniProt: 735-800                          -------------------------------Exon 1.17a UniProt: 832-906  Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.14  PDB: A:6-24 [INCOMPLETE]   ----------------------------------------------------------------Exon 1.16  PDB: A:89-121         --------------------------- Transcript 1 (2)
                 1x5i A   1 GS----------SGS--------------------------SGPATDWLSAETFESDLDETRVPEVPSSLHVRPLVTSIVVSWTPPENQNIVVRGYAIGYGIGSPHAQTIKVDYKQRYYTIENLDPSSHYVITLKAFNNVGEGIPLYESAVTRPHTSG----------------------PSSG 126
                             |       -  | |    -         -         - |      14        24        34        44        54        64        74        84        94       104       114       | -         -         -|   
                             2          3 5                          6                                                                                                                 122                    123   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 1X5I)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: E-set (290)

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain A   (NEO1_HUMAN | Q92859)
molecular function
    GO:0039706    co-receptor binding    Interacting selectively and non-covalently with a coreceptor. A coreceptor acts in cooperation with a primary receptor to transmit a signal within the cell.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    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:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or 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.
    GO:0030513    positive regulation of BMP signaling pathway    Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity.
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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0098797    plasma membrane protein complex    Any protein complex that is part of the plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NEO1_HUMAN | Q928591x5f 1x5g 1x5h 1x5j 1x5k 3p4l

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