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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SMAUG RNA BINDING DOMAIN
 
Authors :  J. B. Green, C. D. Gardner, R. P. Wharton, A. K. Aggarwal
Date :  02 Apr 03  (Deposition) - 08 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Sam Domain, Phat Domain, Rna-Binding Protein, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. B. Green, C. D. Gardner, R. P. Wharton, A. K. Aggarwal
Rna Recognition Via The Sam Domain Of Smaug.
Mol. Cell V. 11 1537 2003
PubMed-ID: 12820967  |  Reference-DOI: 10.1016/S1097-2765(03)00178-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA-BINDING PROTEIN SMAUG
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET 15B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRNA BINDING DOMAIN, SAM DOMAIN
    GeneSMG
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:170
 aligned with SMG_DROME | Q23972 from UniProtKB/Swiss-Prot  Length:999

    Alignment length:170
                                   603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763
            SMG_DROME   594 RNVGMSGIGLWLKSLRLHKYIELFKNMTYEEMLLITEDFLQSVGVTKGASHKLALCIDKLKERANILNRVEQELLSGQMELSTAVEELTNIVLTPMKPLESPGPPEENIGLRFLKVIDIVTNTLQQDPYAVQDDETLGVLMWILDRSIHNEAFMNHASQLKDLKFKLSKM 763
               SCOP domains d1oxja1 A:594-655 RNA-binding protein Smaug                   d1oxja2 A:656-763 RNA-binding protein Smaug                                                                  SCOP domains
               CATH domains 1oxjA01 A:594-654 Transcription Factor, Ets-1                1oxjA02 A:655-763  [code=1.25.40.170, no name defined]                                                        CATH domains
               Pfam domains --SAM_1-1oxjA01 A:596-654                                    -PHAT-1oxjA02 A:656-763                                                                                       Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oxj A 594 HMVGMSGIGLWLKSLRLHKYIELFKNMTYEEMLLITEDFLQSVGVTKGASHKLALCIDKLKERANILNRVEQELLSGQMELSTAVEELTNIVLTPMKPLESPGPPEENIGLRFLKVIDIVTNTLQQDPYAVQDDETLGVLMWILDRSIHNEAFMNHASQLKDLKFKLSKM 763
                                   603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763

   Legend:   → Mismatch (orange background)
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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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: SAM (26)
(-)
Clan: TPR (230)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SMG_DROME | Q23972)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003730    mRNA 3'-UTR binding    Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0017022    myosin binding    Interacting selectively and non-covalently with any part of a myosin complex; myosins are any of a superfamily of molecular motor proteins that bind to actin and use the energy of ATP hydrolysis to generate force and movement along actin filaments.
    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:0030371    translation repressor activity    Antagonizes ribosome-mediated translation of mRNA into a polypeptide.
    GO:0000900    translation repressor activity, nucleic acid binding    Antagonizes the ribosome-mediated translation of mRNA into a polypeptide via direct binding (through a selective and non-covalent interaction) to nucleic acid.
biological process
    GO:0051236    establishment of RNA localization    The directed movement of RNA to a specific location.
    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: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:0000289    nuclear-transcribed mRNA poly(A) tail shortening    Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
    GO:0060213    positive regulation of nuclear-transcribed mRNA poly(A) tail shortening    Any process that increases the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length.
    GO:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
cellular component
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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