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(-) Description

Title :  SOLUTION STRUCTURE OF THE SH3 DOMAIN OF MOUSE PEROXISOMAL BIOGENESIS FACTOR 13
 
Authors :  M. Yoneyama, M. Sato, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  01 Feb 05  (Deposition) - 01 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Sh3 Domain, Pex13, Protein-Protein Interaction, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Nppsfa, National Project On Protein Structural And Functional Analyses, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Yoneyama, M. Sato, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Sh3 Domain Of Mouse Peroxisomal Biogenesis Factor 13
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXISOMAL BIOGENESIS FACTOR 13
    ChainsA
    EngineeredYES
    Expression System PlasmidP040802-03
    Expression System Vector TypePLASMID
    FragmentSH3 DOMAIN
    GenePEX13
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    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 1WXU)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.PEX13_MOUSE274-338  1A:15-79

(-) Exons   (0, 0)

(no "Exon" information available for 1WXU)

(-) 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:93
 aligned with PEX13_MOUSE | Q9D0K1 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:192
                                   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395  
          PEX13_MOUSE   206 GSENEDLWAESEGTVACLSAEDQATNSAKSWPIFLFFAVILGGPYLIWKLLSTHNDEVTDNTNWASGEDDHVVARAEYDFVAVSDEEISFRAGDMLNLALKEQQPKVRGWLLASLDGQTTGLIPANYVKILGKRRGRKTIESSTMLKQQQSFTNPTLIKGVTTTNPLDEQEAAFESVFVETNKVSSAPDSTG 397
               SCOP domains d1      wxua_                                                 A: automated matches                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------1wxuA01 A:16-81 SH3 Domains                                       --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------SH3_1-1wxuA01 A:21-71                              ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------.....------------------------------------------------............eee....................ee............eeee......eee....eee............-----------..----------------------------------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------SH3  PDB: A:15-79 UniProt: 274-338                               ----------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wxu A   1 GS------SGSSG------------------------------------------------TNWASGEDDHVVARAEYDFVAVSDEEISFRAGDMLNLALKEQQPKVRGWLLASLDGQTTGLIPANYVKILGKRRGRKTIES-----------GP----------------------------------SSG  93
                             |      |4  |      -         -         -         -         - |      16        26        36        46        56        66        76        86 |       -   ||    -         -         -        91  
                             2      3   7                                                8                                                                              88          89|                                 91  
                                                                                                                                                                                     90                                     

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  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, 1)

NMR Structure
(-)
Clan: SH3 (175)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (PEX13_MOUSE | Q9D0K1)
molecular function
    GO:0000268    peroxisome targeting sequence binding    Interacting selectively and non-covalently with a peroxisomal targeting sequence, any of several sequences of amino acids within a protein that can act as a signal for the localization of the protein into the peroxisome.
biological process
    GO:0021795    cerebral cortex cell migration    The orderly movement of cells from one site to another in the cerebral cortex.
    GO:0001561    fatty acid alpha-oxidation    A metabolic pathway by which 3-methyl branched fatty acids are degraded. These compounds are not degraded by the normal peroxisomal beta-oxidation pathway, because the 3-methyl blocks the dehydrogenation of the hydroxyl group by hydroxyacyl-CoA dehydrogenase. The 3-methyl branched fatty acid is converted in several steps to pristenic acid, which can then feed into the beta-oxidative pathway.
    GO:0007626    locomotory behavior    The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
    GO:0060152    microtubule-based peroxisome localization    The microtubule-based process in which a peroxisome is transported to, and/or maintained in, a specific location. A peroxisome is a small membrane-bounded organelle that uses dioxygen (O2) to oxidize organic 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:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0098779    positive regulation of macromitophagy in response to mitochondrial depolarization    The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
    GO:0016560    protein import into peroxisome matrix, docking    The process in which a complex formed of a peroxisome targeting sequence (PTS) receptor bound to a PTS-bearing protein docks with translocation machinery in the peroxisomal membrane.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0001967    suckling behavior    Specific behavior of a newborn or infant mammal that results in the derivation of nourishment from the breast.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0098792    xenophagy    The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
    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:0005779    integral component of peroxisomal membrane    The component of the peroxisomal 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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005778    peroxisomal membrane    The lipid bilayer surrounding a peroxisome.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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