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(-) Description

Title :  SOLUTION STRUCTURE OF THE RNA RECOGNITION MOTIF FROM HYPOTHETICAL RNA BINDING PROTEIN BC052180
 
Authors :  T. Nagata, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rna Recognition Motif, Rrm, Rna Binding Domain, Rbd, Rnp, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nagata, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The Rna Recognition Motif From Hypothetical Rna Binding Protein Bc052180
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN RIKEN CDNA 1810017N16
    Chains: A
    Engineered: YES
    Expression System Plasmid: P030916-18
    Expression System Vector Type: PLASMID
    Fragment: RNA RECOGNITION MOTIF
    Gene: RIKEN CDNA 1810017N16
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: HYPOTHETICAL PROTEIN BC052180

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.RB15B_MOUSE136-212
333-410
414-488		  1-
-
A:91-164

(-) Exons   (0, 0)

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(-) 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:97
 aligned with RB15B_MOUSE | Q6PHZ5 from UniProtKB/Swiss-Prot  Length:887

    Alignment length:143
                                   379       389       399       409       419       429       439       449       459       469       479       489       499       509   
          RB15B_MOUSE   370 GQGGAYAFLKFQNLDMAHRAKVAMSGRVIGRNPIKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKAEETRYPQQYQPSPLPVHYELLTDG 512
               SCOP domains d1why                   a_         A: Putative RNA-binding protein 15B, Rbm15b                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------RRM_1-1whyA01 A:93-155                                         ---------------------------------- Pfam domains
         Sec.struct. author .....-------------------..--------............eeee.......hhhhhhhhh....eeeeee......eeeee..hhhhhhhhhhh............eeee...---------...----------.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM  PDB: - UniProt: 333-410             ---RRM  PDB: A:91-164 UniProt: 414-488                                        ------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1why A  74 GSSGS-------------------SG--------KIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS---------GPS----------SG 170
                                |    -         -    ||   -    |   86        96       106       116       126       136       146       156        |-       167|        - | 
                               78                  79|       81                                                                                 165       166 |        169 
                                                    80                                                                                                      168
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 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 1WHY)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: RRM (206)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (RB15B_MOUSE | Q6PHZ5)
molecular function
    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: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: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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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.

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