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(-) Description

Title :  SOLUTION STRUCTURE OF RNA BINDING DOMAIN IN HYPOTHETICAL PROTEIN FLJ11016
 
Authors :  K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  19 May 05  (Deposition) - 19 Nov 05  (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, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of Rna Binding Domain In Hypothetical Protein Flj11016
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN FLJ11016
    Chains: A
    Engineered: YES
    Expression System Plasmid: P040816-17
    Expression System Vector Type: PLASMID
    Fragment: RNA RECOGNITION MOTIF
    Gene: FLJ11016
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-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 2CPX)

(-) Sites  (0, 0)

(no "Site" information available for 2CPX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_028897H376YRBM41_HUMANPolymorphism17850127AY376Y
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.RBM41_HUMAN309-387  1A:309-387

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003724791bENSE00001092587X:106362034-10636199639RBM41_HUMAN1-330--
1.2bENST000003724792bENSE00000866531X:106359996-106359880117RBM41_HUMAN3-42400--
1.4ENST000003724794ENSE00000866529X:106359284-106359092193RBM41_HUMAN42-106650--
1.5aENST000003724795aENSE00000866528X:106358786-106358582205RBM41_HUMAN107-175690--
1.8cENST000003724798cENSE00000674313X:106332069-106331666404RBM41_HUMAN175-3091351A:284-309 (gaps)85
1.9dENST000003724799dENSE00001212903X:106312632-106312485148RBM41_HUMAN310-359501A:310-35950
1.10bENST0000037247910bENSE00001457910X:106310923-106310368556RBM41_HUMAN359-413551A:359-398 (gaps)54

(-) 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 RBM41_HUMAN | Q96IZ5 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:188
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404        
          RBM41_HUMAN   225 GDSGTAESPSLLQDKGKQAAQGKGPSLHVANVIDFSPEQCWTGPKKLTQPIEFVPEDEIQRNRLSEEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFGKNKKQRSNLQATSLISCATGSTTEISG 412
               SCOP domains ------------------------------------------------------------------d2cpxa1 A:291-392 RNA-binding protein 41, RBM41                                                       -------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......---------.--------------------------------------------------...................eeeee......hhhhhhhhhhhhhhh.....eeeee......eeeee..hhhhhhhhhhhh..........eeee........-----------....---.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------Y------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------RRM  PDB: A:309-387 UniProt: 309-387                                           ------------------------- PROSITE
           Transcript 1 (1) Exon 1.8c  PDB: A:284-309 (gaps) UniProt: 175-309 [INCOMPLETE]                       -------------------------------------------------Exon 1.10b  PDB: A:359-398 (gaps) UniProt: 359-413     Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------Exon 1.9d  PDB: A:310-359 UniProt: 310-359        ----------------------------------------------------- Transcript 1 (2)
                 2cpx A 284 GSSGSS---------G--------------------------------------------------EEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRS-----------SGPS---SG 398
                                 |   -     |   -         -         -         -         -      |294       304       314       324       334       344       354       364       374       384       | -       393  |   | 
                               289       290                                                291                                                                                                  392         393  | 397 
                                                                                                                                                                                                                396
   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 2CPX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain A   (RBM41_HUMAN | Q96IZ5)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0030626    U12 snRNA binding    Interacting selectively and non-covalently with the U12 small nuclear RNA (U12 snRNA).
    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: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:0032502    developmental process    A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
    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.
cellular component
    GO:0005689    U12-type spliceosomal complex    Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron; the series of U12-type spliceosomal complexes is involved in the splicing of the majority of introns that contain atypical AT-AC terminal dinucleotides, as well as other non-canonical introns. The entire splice site signal, not just the terminal dinucleotides, is involved in determining which spliceosome utilizes the site.

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