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(-) Description

Title :  RRM DOMAIN FROM C. ELEGANS SUP-12
 
Authors :  S. Amrane, C. D. Mackereth
Date :  27 Nov 13  (Deposition) - 03 Sep 14  (Release) - 04 May 16  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  S  (15x)
NMR Structure *:  S  (1x)
Keywords :  Transcription, Development (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Amrane, K. Rebora, I. Zniber, D. Dupuy, C. D. Mackereth
Backbone-Independent Nucleic Acid Binding By Splicing Factor Sup-12 Reveals Key Aspects Of Molecular Recognition
Nat. Commun. V. 5 4595 2014
PubMed-ID: 25183497  |  Reference-DOI: 10.1038/NCOMMS5595

(-) Compounds

Molecule 1 - PROTEIN SUP-12, ISOFORM B
    Chains: S
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-HIS1A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSY
    Expression System Vector Type: PLASMID
    Fragment: RRM DOMAIN, RESIDUES 28 TO 121
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Tissue: MUSCLE

 Structural Features

(-) Chains, Units

  1
NMR Structure (15x): S
NMR Structure * (1x): S

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4CH0)

(-) Sites  (0, 0)

(no "Site" information available for 4CH0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CH0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CH0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CH0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CH0)

(-) Exons   (0, 0)

(no "Exon" information available for 4CH0)

(-) 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 S from PDB  Type:PROTEIN  Length:97
 aligned with H2L051_CAEEL | H2L051 from UniProtKB/TrEMBL  Length:151

    Alignment length:97
                                    34        44        54        64        74        84        94       104       114       
         H2L051_CAEEL    25 PVVGSRDTMFTKIFVGGLPYHTSDKTLHEYFEQFGDIEEAVVITDRNTQKSRGYGFVTMKDRASAERACKDPNPIIDGRKANVNLAYLGAKPRTNVQ 121
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.eeeee......hhhhhhhhhh....eeeeeeee......eeeeeeeee.hhhhhhhhh.....ee..ee.eeeehhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4ch0 S  25 GAMGSRDTMFTKIFVGGLPYHTSDKTLHEYFEQFGDIEEAVVITDRNTQKSRGYGFVTMKDRASAERACKDPNPIIDGRKANVNLAYLGAKPRTNVQ 121
                                    34        44        54        64        74        84        94       104       114       


Chain S from PDB  Type:PROTEIN  Length:97
 aligned with O45189_CAEEL | O45189 from UniProtKB/TrEMBL  Length:248

    Alignment length:97
                                    34        44        54        64        74        84        94       104       114       
         O45189_CAEEL    25 PVVGSRDTMFTKIFVGGLPYHTSDKTLHEYFEQFGDIEEAVVITDRNTQKSRGYGFVTMKDRASAERACKDPNPIIDGRKANVNLAYLGAKPRTNVQ 121
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.eeeee......hhhhhhhhhh....eeeeeeee......eeeeeeeee.hhhhhhhhh.....ee..ee.eeeehhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4ch0 S  25 GAMGSRDTMFTKIFVGGLPYHTSDKTLHEYFEQFGDIEEAVVITDRNTQKSRGYGFVTMKDRASAERACKDPNPIIDGRKANVNLAYLGAKPRTNVQ 121
                                    34        44        54        64        74        84        94       104       114
   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 4CH0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CH0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CH0)

(-) Gene Ontology  (12, 23)

NMR Structure(hide GO term definitions)
Chain S   (H2L051_CAEEL | H2L051)
molecular function
    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.
    GO:0036002    pre-mRNA binding    Interacting selectively and non-covalently with pre-messenger RNA (pre-mRNA), an intermediate molecule between DNA and protein that may contain introns and, at least in part, encodes one or more proteins. Introns are removed from pre-mRNA to form a mRNA molecule.
    GO:0097157    pre-mRNA intronic binding    Interacting selectively and non-covalently with an intronic sequence of a pre-messenger RNA (pre-mRNA).
    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).
biological process
    GO:0000380    alternative mRNA splicing, via spliceosome    The process of generating multiple mRNA molecules from a given set of exons by differential use of exons from the primary transcript(s) to form multiple mature mRNAs that vary in their exon composition.
    GO:0032956    regulation of actin cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0000381    regulation of alternative mRNA splicing, via spliceosome    Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
    GO:0040012    regulation of locomotion    Any process that modulates the frequency, rate or extent of locomotion of a cell or organism.
cellular component
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.

Chain S   (O45189_CAEEL | O45189)
molecular function
    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.
    GO:0036002    pre-mRNA binding    Interacting selectively and non-covalently with pre-messenger RNA (pre-mRNA), an intermediate molecule between DNA and protein that may contain introns and, at least in part, encodes one or more proteins. Introns are removed from pre-mRNA to form a mRNA molecule.
    GO:0097157    pre-mRNA intronic binding    Interacting selectively and non-covalently with an intronic sequence of a pre-messenger RNA (pre-mRNA).
    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:0003727    single-stranded RNA binding    Interacting selectively and non-covalently with single-stranded RNA.
biological process
    GO:0000380    alternative mRNA splicing, via spliceosome    The process of generating multiple mRNA molecules from a given set of exons by differential use of exons from the primary transcript(s) to form multiple mature mRNAs that vary in their exon composition.
    GO:0032956    regulation of actin cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0000381    regulation of alternative mRNA splicing, via spliceosome    Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
    GO:0040012    regulation of locomotion    Any process that modulates the frequency, rate or extent of locomotion of a cell or organism.
cellular component
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.

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 Related Entries

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

UniProtKB/TrEMBL
        H2L051_CAEEL | H2L051: 4ch1
        O45189_CAEEL | O45189: 2mgz 2ru3 4cio

(-) Related Entries Specified in the PDB File

4ch1 RRM DOMAIN FROM C. ELEGANS SUP-12
4cio RRM DOMAIN FROM C. ELEGANS SUP-12 BOUND TO GGUGUGC RNA