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(-) Description

Title :  REFINEMENT OF RNA BINDING DOMAIN IN HUMAN TRA2 BETA PROTEIN
 
Authors :  K. Tsuda, K. Kuwasako, M. Takahashi, T. Someya, M. Inoue, T. Kigawa, T. T M. Shirouzu, S. Sugano, Y. Muto, S. Yokoyama
Date :  17 Jun 10  (Deposition) - 27 Apr 11  (Release) - 27 Apr 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Rrm Domain, Rbd, Rna Binding Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tsuda, T. Someya, K. Kuwasako, M. Takahashi, F. He, S. Unzai, M. Inoue, T. Harada, S. Watanabe, T. Terada, N. Kobayashi, M. Shirouzu T. Kigawa, A. Tanaka, S. Sugano, P. Guntert, S. Yokoyama, Y. Muto
Structural Basis For The Dual Rna-Recognition Modes Of Huma Tra2-Beta Rrm.
Nucleic Acids Res. V. 39 1538 2011
PubMed-ID: 20926394  |  Reference-DOI: 10.1093/NAR/GKQ854

(-) Compounds

Molecule 1 - CDNA FLJ40872 FIS, CLONE TUTER2000283, HIGHLY SIMILAR TO HOMO SAPIENS TRANSFORMER-2-BETA (SFRS10) GENE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: P040517-05
    Expression System Vector Type: VECTOR
    Fragment: RNA RECOGNITION MOTIF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2RRB)

(-) Sites  (0, 0)

(no "Site" information available for 2RRB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.TRA2B_HUMAN118-196  1A:118-196
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.TRA2B_HUMAN118-196  1A:118-196

(-) Exons   (0, 0)

(no "Exon" information available for 2RRB)

(-) 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:96
 aligned with Q8N1H4_HUMAN | Q8N1H4 from UniProtKB/TrEMBL  Length:252

    Alignment length:103
                                    72        82        92       102       112       122       132       142       152       162   
         Q8N1H4_HUMAN    63 SPMSTRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHT 165
               SCOP domains d2r       rba_ A: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------RRM_1-2rrbA01 A:120-190                                                ----------- Pfam domains
         Sec.struct. author ...-------..........eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2rrb A 106 GPL-------GSRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHT 201
                              |      -|      118       128       138       148       158       168       178       188       198   
                              |     109                                                                                            
                            108                                                                                                    


Chain A from PDB  Type:PROTEIN  Length:96
 aligned with TRA2B_HUMAN | P62995 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:103
                                   108       118       128       138       148       158       168       178       188       198   
          TRA2B_HUMAN    99 SPMSTRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHT 201
               SCOP domains d2r       rba_ A: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------RRM_1-2rrbA01 A:120-190                                                ----------- Pfam domains
         Sec.struct. author ...-------..........eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------RRM  PDB: A:118-196 UniProt: 118-196                                           ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2rrb A 106 GPL-------GSRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHT 201
                              |      -|      118       128       138       148       158       168       178       188       198   
                            108     109
   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  (1, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: RRM (206)

(-) Gene Ontology  (14, 16)

NMR Structure(hide GO term definitions)
Chain A   (TRA2B_HUMAN | P62995)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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: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: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:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0000375    RNA splicing, via transesterification reactions    Splicing of RNA via a series of two transesterification reactions.
    GO:0021796    cerebral cortex regionalization    The regionalization process that results in the creation of areas within the cerebral cortex that will direct the behavior of cell migration and differentiation as the cortex develops.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0048026    positive regulation of mRNA splicing, via spliceosome    Any process that activates or increases the rate or extent of mRNA splicing via a spliceosomal mechanism.
    GO:0000381    regulation of alternative mRNA splicing, via spliceosome    Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
cellular component
    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.

Chain A   (Q8N1H4_HUMAN | Q8N1H4)
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.

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  TRA2B_HUMAN | P62995
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q8N1H4_HUMAN | Q8N1H4: 2rra
        TRA2B_HUMAN | P62995: 2cqc 2kxn 2rra

(-) Related Entries Specified in the PDB File

2rra