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(-) Description

Title :  SOLUTION STRUCTURE OF RNA BINDING DOMAIN IN PRE-MRNA-SPLICING FACTOR RBM22
 
Authors :  N. Kasahara, K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  05 Apr 07  (Deposition) - 09 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rrm Domain, Rbd, 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 :  N. Kasahara, K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of Rna Binding Domain In Pre-Mrna-Splicing Factor Rbm22
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PRE-MRNA-SPLICING FACTOR RBM22
    ChainsA
    EngineeredYES
    Expression System PlasmidP060313-05
    Expression System Vector TypePLASMID
    FragmentRNA BINDING MOTIF
    GeneRBM22
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymRNA-BINDING MOTIF PROTEIN 22, ZINC FINGER CCCH DOMAIN-CONTAINING PROTEIN 16

 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 2YTC)

(-) Sites  (0, 0)

(no "Site" information available for 2YTC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_C3H1PS50103 Zinc finger C3H1-type profile.RBM22_HUMAN159-186  1A:233-234
2RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.RBM22_HUMAN232-305  1A:239-311

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000001998141aENSE00002132423chr5:150080669-150080494176RBM22_HUMAN1-18180--
1.2cENST000001998142cENSE00000906343chr5:150080059-15008000654RBM22_HUMAN19-36180--
1.3bENST000001998143bENSE00000906344chr5:150078833-15007880430RBM22_HUMAN37-46100--
1.4ENST000001998144ENSE00000906345chr5:150078193-150078061133RBM22_HUMAN47-91450--
1.5aENST000001998145aENSE00002195629chr5:150076453-150076353101RBM22_HUMAN91-124340--
1.5dENST000001998145dENSE00001506412chr5:150076267-150076095173RBM22_HUMAN125-182581A:227-234 (gaps)40
1.6bENST000001998146bENSE00000841232chr5:150075268-150075068201RBM22_HUMAN182-249681A:235-25622
1.7bENST000001998147bENSE00000767641chr5:150073802-150073638165RBM22_HUMAN249-304561A:256-31156
1.8ENST000001998148ENSE00000767642chr5:150072869-15007278189RBM22_HUMAN304-334311A:311-3111
1.9ENST000001998149ENSE00000767643chr5:150072588-150072457132RBM22_HUMAN334-378450--
1.10bENST0000019981410bENSE00001085702chr5:150071443-1500703561088RBM22_HUMAN378-420430--

(-) 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:85
 aligned with RBM22_HUMAN | Q9NW64 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:167
                                   147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       
          RBM22_HUMAN   138 GKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKRASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR 304
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------RRM_1-2ytcA01 A:241-306                                           ----- Pfam domains
         Sec.struct. author ......--------------------------------..--------------------------------------------------......eeee......hhhhhhhhhhh...eeeeeeehhh.eeeeee.hhhhhhhhhhh.....ee..ee..eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------ZF_C3H1  PDB: A:233-234     ---------------------------------------------RRM  PDB: A:239-311 UniProt: 232-305                                      PROSITE
           Transcript 1 (1) Exon 1.5d  PDB: A:227-234 (gaps) [INCOMPLETE]------------------------------------------------------------------Exon 1.7b  PDB: A:256-311 UniProt: 249-304               Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.6b  PDB: A:235-256 UniProt: 182-249 [INCOMPLETE]             ------------------------------------------------------1 Transcript 1 (2)
                 2ytc A 227 GSSGSS--------------------------------GE--------------------------------------------------DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR 311
                                 |   -         -         -       234         -         -         -         -         -|      244       254       264       274       284       294       304       
                               232                              233|                                                235                                                                            
                                                                 234                                                                                                                               

   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 2YTC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: RRM (206)

(-) Gene Ontology  (27, 27)

NMR Structure(hide GO term definitions)
Chain A   (RBM22_HUMAN | Q9NW64)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0017070    U6 snRNA binding    Interacting selectively and non-covalently with the U6 small nuclear RNA (U6 snRNA).
    GO:0048306    calcium-dependent 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), in the presence of calcium.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0005487    nucleocytoplasmic transporter activity    Enables the directed movement of substances between the nucleus and the cytoplasm of a cell.
    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: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:0035690    cellular response to drug    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0045292    mRNA cis splicing, via spliceosome    The joining together, after removal of an intervening sequence composed of one or more introns, of two segments of the same RNA molecule via spliceosomal catalysis to produce an mRNA composed only of exon sequences that all came from the same primary transcript.
    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:0033120    positive regulation of RNA splicing    Any process that activates or increases the frequency, rate or extent of RNA splicing.
    GO:0090316    positive regulation of intracellular protein transport    Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells.
    GO:0000060    protein import into nucleus, translocation    A protein transport process that contributes to protein import into the nucleus, and that results in the vectorial transfer of a cargo-carrier protein complex through the nuclear pore complex from the cytoplasmic side to the nucleoplasmic side of the nuclear envelope.
    GO:0000387    spliceosomal snRNP assembly    The aggregation, arrangement and bonding together of one or more snRNA and multiple protein components to form a ribonucleoprotein complex that is involved in formation of the spliceosome.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0000974    Prp19 complex    A protein complex consisting of Prp19 and associated proteins that is involved in the transition from the precatalytic spliceosome to the activated form that catalyzes step 1 of splicing, and which remains associated with the spliceosome through the second catalytic step. It is widely conserved, found in both yeast and mammals, though the exact composition varies. In S. cerevisiae, it contains Prp19p, Ntc20p, Snt309p, Isy1p, Syf2p, Cwc2p, Prp46p, Clf1p, Cef1p, and Syf1p.
    GO:0071006    U2-type catalytic step 1 spliceosome    A spliceosomal complex that is formed by the displacement of the U1 and U4 snRNPs from the precatalytic spliceosome; the U2, U5 and U6 snRNPs remain associated with the mRNA. This complex, sometimes called the activated spliceosome, is the catalytically active form of the spliceosome, and includes many proteins in addition to those found in the U2, and U5 and U6 snRNPs.
    GO:0071007    U2-type catalytic step 2 spliceosome    A spliceosomal complex that contains the U2, U5 and U6 snRNPs bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the U2, U5 and U6 snRNPs.
    GO:0071013    catalytic step 2 spliceosome    A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.
    GO:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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 Related Entries

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        RBM22_HUMAN | Q9NW645mqf

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