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(-) Description

Title :  SOLUTION STRUCTURE OF THE SIXTH FIBRONECTIN TYPE III DOMAIN OF HUMAN NETRIN RECEPTOR DCC
 
Authors :  N. Tochio, S. Koshiba, T. Tomizawa, M. Yoneyama, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 Feb 07  (Deposition) - 04 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Tumor Suppressor Protein Dcc, Colorectal Cancer Suppressor, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Tochio, S. Koshiba, T. Tomizawa, M. Yoneyama, T. Kigawa, S. Yokoyama
Solution Structure Of The Sixth Fibronectin Type Iii Domain Of Human Netrin Receptor Dcc
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NETRIN RECEPTOR DCC
    ChainsA
    EngineeredYES
    Expression System PlasmidP050905-24
    Expression System Vector TypePLASMID
    FragmentSIXTH FN3 DOMAIN
    GeneDCC
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymTUMOR SUPPRESSOR PROTEIN DCC, COLORECTAL CANCER SUPPRESSOR

 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 2EDE)

(-) Sites  (0, 0)

(no "Site" information available for 2EDE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EDE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

NMR Structure (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024495M1017VDCC_HUMANPolymorphism984274AM81V
2UniProtVAR_035511F1039SDCC_HUMANUnclassified  ---AF103S
3CancerSNPVAR_DCC_HUMAN_CCDS11952_1_01 *F1039SDCC_HUMANDisease (Colorectal cancer)  ---AF103S
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.DCC_HUMAN431-524
530-620
625-718
728-821
846-942
947-1044
  1-
-
-
-
-
A:11-108

(-) Exons   (0, 0)

(no "Exon" information available for 2EDE)

(-) 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:114
 aligned with DCC_HUMAN | P43146 from UniProtKB/Swiss-Prot  Length:1447

    Alignment length:119
                                   946       956       966       976       986       996      1006      1016      1026      1036      1046         
           DCC_HUMAN    937 ATTYEAAPTSAPKDLTVITREGKPRAVIVSWQPPLEANGKITAYILFYTLDKNIPIDDWIMETISGDRLTHQIMDLNLDTMYYFRIQARNSKGVGPLSDPILFRTLKVEHPDKMANDQG 1055
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeee.......eeeeee..........eeeeeee..........eeeeee....eeee.......eeeeeeeee...........eeee........-----.. Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------------------------------V---------------------S---------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------S---------------- SAPs(SNPs) (2)
                    PROSITE FN3   ----FN3  PDB: A:11-108 UniProt: 947-1044                                                              ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                2ede A    1 GSSGSSGPTSAPKDLTVITREGKPRAVIVSWQPPLEANGKITAYILFYTLDKNIPIDDWIMETISGDRLTHQIMDLNLDTMYYFRIQARNSKGVGPLSDPILFRTLKVSGPS-----SG  114
                                    10        20        30        40        50        60        70        80        90       100       110 |     | 
                                                                                                                                         112   113 

   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  (0, 0)

(no "SCOP Domain" information available for 2EDE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2EDE)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (DCC_HUMAN | P43146)
molecular function
    GO:0005042    netrin receptor activity    Combining with a netrin signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    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:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
    GO:0033564    anterior/posterior axon guidance    The process in which the migration of an axon growth cone is directed to a specific target site along the anterior-posterior body axis in response to a combination of attractive and repulsive cues. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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: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:0033563    dorsal/ventral axon guidance    The process in which the migration of an axon growth cone is directed to a specific target site along the dorsal-ventral body axis in response to a combination of attractive and repulsive cues. 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:0097192    extrinsic apoptotic signaling pathway in absence of ligand    A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0048671    negative regulation of collateral sprouting    Any process that stops, prevents, or reduces the frequency, rate or extent of collateral sprouting.
    GO:2000171    negative regulation of dendrite development    Any process that stops, prevents, or reduces the frequency, rate or extent of dendrite development.
    GO:0010977    negative regulation of neuron projection development    Any process that decreases 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: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:0038007    netrin-activated signaling pathway    A series of molecular events initiated by the binding of a netrin protein to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Netrins can act as chemoattractant signals for some cells and chemorepellent signals for others. Netrins also have roles outside of cell and axon guidance.
    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:1901214    regulation of neuron death    Any process that modulates the frequency, rate or extent of neuron death.
    GO:0021965    spinal cord ventral commissure morphogenesis    The process in which the anatomical structures of the spinal cord ventral commissure are generated and organized.
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DCC_HUMAN | P431462ed7 2ed8 2ed9 2edb 2edd 3au4 4urt

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