Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE FIRST FIBRONECTIN TYPE III DOMAIN OF HUMAN KIAA0343 PROTEIN
 
Authors :  C. Zhao, T. Kigawa, Y. Muto, S. Koshiba, N. Tochio, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  22 May 03  (Deposition) - 22 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Immunoglobulin-Like Beta-Sandwich Fold, Ng-Cam Related Cell Adhesion Molecule, Fibronectin Type Iii Domain, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Zhao, T. Kigawa, Y. Muto, S. Koshiba, N. Tochio, M. Inoue, S. Yokoyama
Solution Structure Of The First Fibronectin Type Iii Domain Of Human Kiaa0343 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KIAA0343 PROTEIN
    ChainsA
    EngineeredYES
    Expression System PlasmidP021007-30
    Expression System Vector TypePLASMID
    FragmentFIBRONECTIN TYPE III DOMAIN
    GeneKAZUSA CDNA HG01457
    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 1UEY)

(-) Sites  (0, 0)

(no "Site" information available for 1UEY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.NRCAM_HUMAN649-744
746-843
848-950
954-1051
1064-1156
  2A:19-114
A:116-127
-
-
-

(-) Exons   (6, 6)

NMR Structure (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003790282bENSE00001352873chr7:108096826-108096687140NRCAM_HUMAN-00--
1.3ENST000003790283ENSE00001352872chr7:108040037-108039880158NRCAM_HUMAN-00--
1.6ENST000003790286ENSE00001352869chr7:107953175-10795310967NRCAM_HUMAN-00--
1.8aENST000003790288aENSE00001352863chr7:107880614-107880403212NRCAM_HUMAN1-36360--
1.9bENST000003790289bENSE00001654208chr7:107878213-10787819618NRCAM_HUMAN36-4270--
1.10bENST0000037902810bENSE00000881822chr7:107875132-107875027106NRCAM_HUMAN42-77360--
1.11dENST0000037902811dENSE00000881820chr7:107872966-107872770197NRCAM_HUMAN77-143670--
1.12ENST0000037902812ENSE00000881818chr7:107871597-107871475123NRCAM_HUMAN143-184420--
1.13ENST0000037902813ENSE00000881815chr7:107866822-107866652171NRCAM_HUMAN184-241580--
1.14ENST0000037902814ENSE00000881814chr7:107866145-10786608957NRCAM_HUMAN241-260200--
1.15ENST0000037902815ENSE00000881813chr7:107864280-107864169112NRCAM_HUMAN260-297380--
1.16aENST0000037902816aENSE00000881810chr7:107850049-107849865185NRCAM_HUMAN297-359630--
1.17aENST0000037902817aENSE00000881808chr7:107848103-107847972132NRCAM_HUMAN359-403450--
1.18bENST0000037902818bENSE00000881807chr7:107838543-107838400144NRCAM_HUMAN403-451490--
1.19ENST0000037902819ENSE00000881805chr7:107836316-107836205112NRCAM_HUMAN451-488380--
1.20ENST0000037902820ENSE00000716775chr7:107834872-107834706167NRCAM_HUMAN488-544570--
1.21ENST0000037902821ENSE00000716774chr7:107834615-107834468148NRCAM_HUMAN544-593500--
1.22ENST0000037902822ENSE00000881802chr7:107832297-107832173125NRCAM_HUMAN593-635431A:1-77
1.23ENST0000037902823ENSE00001479582chr7:107831727-10783169830NRCAM_HUMAN635-645111A:8-158
1.24ENST0000037902824ENSE00000716772chr7:107830190-107830089102NRCAM_HUMAN645-679351A:15-4935
1.25ENST0000037902825ENSE00000881799chr7:107825058-107824861198NRCAM_HUMAN679-745671A:49-11567
1.26ENST0000037902826ENSE00000881798chr7:107824755-10782468571NRCAM_HUMAN745-768241A:115-124 (gaps)16
1.27bENST0000037902827bENSE00000716769chr7:107823364-107823139226NRCAM_HUMAN769-844761A:125-1273
1.28ENST0000037902828ENSE00000881796chr7:107822381-107822266116NRCAM_HUMAN844-882390--
1.29ENST0000037902829ENSE00000881795chr7:107820871-107820667205NRCAM_HUMAN883-951690--
1.31bENST0000037902831bENSE00000881794chr7:107818557-107818435123NRCAM_HUMAN951-992420--
1.33ENST0000037902833ENSE00001669101chr7:107817051-107816875177NRCAM_HUMAN992-1051600--
1.34ENST0000037902834ENSE00001479555chr7:107815802-10781576736NRCAM_HUMAN1051-1063130--
1.35ENST0000037902835ENSE00001665448chr7:107808847-107808722126NRCAM_HUMAN1063-1105430--
1.36ENST0000037902836ENSE00001479549chr7:107807518-107807366153NRCAM_HUMAN1105-1156520--
1.37ENST0000037902837ENSE00001691369chr7:107800937-107800806132NRCAM_HUMAN1156-1200450--
1.38ENST0000037902838ENSE00000716759chr7:107799986-10779990879NRCAM_HUMAN1200-1226270--
1.41hENST0000037902841hENSE00001352665chr7:107790592-1077880822511NRCAM_HUMAN1226-1304790--

(-) 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:127
 aligned with NRCAM_HUMAN | Q92823 from UniProtKB/Swiss-Prot  Length:1304

    Alignment length:172
                                   615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775  
          NRCAM_HUMAN   606 VSDDDSGTYTCVANTTLDSVSASAVLSVVAPTPTPAPVYDVPNPPFDLELTDQLDKSVQLSWTPGDDNNSPITKFIIEYEDAMHKPGLWHHQTEVSGTQTTAQLKLSPYVNYSFRVMAVNSIGKSLPSEASEQYLTKASEPDKNPTAVEGLGSEPDNLVITWKPLNGFESNG 777
               SCOP domains d1ueya_                          A: KIAA0343 protein                                                                                                                         SCOP domains
               CATH domains 1ueyA00                          A:1-127 Immunoglobulins                                                                                                                     CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------fn3--------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------fn3--------------------------- Pfam domains (2)
         Sec.struct. author .......-------------------------.............eeeeee......eeeeee........eeeeeeeee........eeeeeeee....eeee......eeeeeeeeee.............ee...........------...--------------... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------FN3  PDB: A:19-114 UniProt: 649-744                                                             -FN3  PDB: A:116-127              PROSITE
           Transcript 1 (1) Exon 1.22  PDB: A:1-7         ---------Exon 1.24  PDB: A:15-49            -----------------------------------------------------------------Exon 1.26 [INCOMPLETE]  1.27b     Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.23  ---------------------------------Exon 1.25  PDB: A:49-115 UniProt: 679-745                          -------------------------------- Transcript 1 (2)
                 1uey A   1 GSSGSSG-------------------------PTPAPVYDVPNPPFDLELTDQLDKSVQLSWTPGDDNNSPITKFIIEYEDAMHKPGLWHHQTEVSGTQTTAQLNLSPYVNYSFRVMAVNSIGKSLPSEASEQYLTKASEPDKNPT------SGP--------------SSG 127
                                  |  -         -         -  |     15        25        35        45        55        65        75        85        95       105       115     |   -  | |    -       125  
                                  7                         8                                                                                                              121    122 |            125  
                                                                                                                                                                                    124                 

   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  (1, 2)

NMR Structure
(-)
Clan: E-set (290)
(-)
Family: fn3 (66)
1afn3-1ueyA01A:118-121
1bfn3-1ueyA02A:118-121

(-) Gene Ontology  (31, 31)

NMR Structure(hide GO term definitions)
Chain A   (NRCAM_HUMAN | Q92823)
molecular function
    GO:0030506    ankyrin binding    Interacting selectively and non-covalently with ankyrin, a 200 kDa cytoskeletal protein that attaches other cytoskeletal proteins to integral membrane proteins.
    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).
    GO:0086080    protein binding involved in heterotypic cell-cell adhesion    Interacting selectively and non-covalently with any protein or protein complex contributing to the adhesion of two different types of cells.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    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:0007413    axonal fasciculation    The collection of axons into a bundle of rods, known as a fascicle.
    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: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: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:0045162    clustering of voltage-gated sodium channels    The process in which voltage-gated sodium channels become localized together in high densities. In animals, nodes of Ranvier differ dramatically from internodal axonal regions in very high densities of voltage-dependent sodium (Nav) channels responsible for the rapid, inward ionic currents that produce membrane depolarization.
    GO:0034113    heterotypic cell-cell adhesion    The attachment of a cell to a cell of a different type via adhesion molecules.
    GO:0001764    neuron migration    The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature.
    GO:0019227    neuronal action potential propagation    The propagation of an action potential along an axon, away from the soma.
    GO:0045666    positive regulation of neuron differentiation    Any process that activates or increases the frequency, rate or extent of neuron differentiation.
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0030516    regulation of axon extension    Any process that modulates the rate, direction or extent of axon extension.
    GO:0010975    regulation of neuron projection development    Any process that modulates the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0031290    retinal ganglion cell axon guidance    The process in which the migration of an axon growth cone of a retinal ganglion cell (RGC) is directed to its target in the brain in response to a combination of attractive and repulsive cues.
    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.
    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:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0043194    axon initial segment    Portion of the axon proximal to the neuronal cell body, at the level of the axon hillock. The action potentials that propagate along the axon are generated at the level of this initial segment.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1uey)
 
  Sites
(no "Sites" information available for 1uey)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1uey)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1uey
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NRCAM_HUMAN | Q92823
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  NRCAM_HUMAN | Q92823
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NRCAM_HUMAN | Q928231uen

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1UEY)