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(-) Description

Title :  SOLUTION STRUCTURE OF THE RNA BINDING DOMAIN IN CYTOTOXIC GRANULE-ASSOCIATED RNA BINDING PROTEIN 1
 
Authors :  C. Abe, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 Mar 06  (Deposition) - 15 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rrm Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Abe, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOTOXIC GRANULE-ASSOCIATED RNA BINDING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050425-20
    Expression System Vector TypePLASMID
    FragmentRNA RECOGNITION MOTIF
    GeneTIA1
    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 2DGO)

(-) Sites  (0, 0)

(no "Site" information available for 2DGO)

(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DGO)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.TIA1_MOUSE7-83
106-184
214-286
  2-
A:78-156
A:176-177

(-) Exons   (0, 0)

(no "Exon" information available for 2DGO)

(-) 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:115
 aligned with TIA1_MOUSE | P52912 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:157
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       
           TIA1_MOUSE    68 GRKIMGKEVKVNWATTPSSQKKDTSSSTVVSTQRSQDHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQLSYDEVVSQSSPNNCTVYCGGVTSG 224
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .------------............-----------..eeeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhh...ee..ee.eeee.................---------....----------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM  PDB: -     ----------------------RRM  PDB: A:78-156 UniProt: 106-184                                            -----------------------------RRM         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dgo A  63 G------------SSGSSGQKKDTS-----------NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTK---------QSGP----------SSG 177
                            |        -   |    70    |    -      | 79        89        99       109       119       129       139       149       159       169|        -|  |     -    |  
                            |           64         75          76                                                                                           170       171  |        175  
                           63                                                                                                                                            174             

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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (TIA1_MOUSE | P52912)
molecular function
    GO:0017091    AU-rich element binding    Interacting selectively and non-covalently with a region of RNA containing frequent adenine and uridine bases.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    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:0042036    negative regulation of cytokine biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cytokines.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:1904037    positive regulation of epithelial cell apoptotic process    Any process that activates or increases the frequency, rate or extent of epithelial cell apoptotic process.
    GO:1903608    protein localization to cytoplasmic stress granule    A process in which a protein is transported to, or maintained in, a location within a cytoplasmic stress granule.
    GO:0048024    regulation of mRNA splicing, via spliceosome    Any process that modulates the frequency, rate or extent of mRNA splicing via a spliceosomal mechanism.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0010494    cytoplasmic stress granule    A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0097165    nuclear stress granule    A dense aggregation in the nucleus composed of proteins and RNAs that appear when the cell is under stress.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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        TIA1_MOUSE | P529122rne

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