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(-) Description

Title :  SOLUTION STRUCTURE OF THE PWI MOTIF FROM SRM160
 
Authors :  B. R. Szymczyna, J. Bowman, S. Mccracken, A. Pineda-Lucena, Y. Lu, B. Cox, M. Lambermon, B. R. Graveley, C. H. Arrowsmith, B. J. Blencowe
Date :  11 Sep 02  (Deposition) - 16 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Four Helix Bundle, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. R. Szymczyna, J. Bowman, S. Mccracken, A. Pineda-Lucena, Y. Lu, B. Cox, M. Lambermon, B. R. Graveley, C. H. Arrowsmith, B. J. Blencowe
Structure And Function Of The Pwi Motif: A Novel Nucleic Acid-Binding Domain That Facilitates Pre-Mrna Processing.
Genes Dev. V. 17 461 2003
PubMed-ID: 12600940  |  Reference-DOI: 10.1101/GAD.1060403
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SER/ARG-RELATED NUCLEAR MATRIX PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21-GOLD (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPWI MOTIF (RESIDUES 27-134)
    GeneSRM160
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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 1MP1)

(-) Sites  (0, 0)

(no "Site" information available for 1MP1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MP1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MP1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MP1)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PWIPS51025 PWI domain profile.SRRM1_HUMAN27-126  1A:27-126

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4aENST000003238484aENSE00002145508chr1:24969594-24969838245SRRM1_HUMAN1-770--
1.5ENST000003238485ENSE00001768046chr1:24972475-2497256490SRRM1_HUMAN8-37301A:24-37 (gaps)20
1.6aENST000003238486aENSE00001717192chr1:24973158-24973280123SRRM1_HUMAN38-78411A:38-7841
1.6hENST000003238486hENSE00001701767chr1:24975350-24975520171SRRM1_HUMAN79-135571A:79-13456
1.7bENST000003238487bENSE00001036950chr1:24976462-24976577116SRRM1_HUMAN136-174390--
1.9aENST000003238489aENSE00000839641chr1:24977900-24978103204SRRM1_HUMAN174-242690--
1.10dENST0000032384810dENSE00000839643chr1:24978925-24979119195SRRM1_HUMAN242-307660--
1.11aENST0000032384811aENSE00000839644chr1:24979404-24979523120SRRM1_HUMAN307-347410--
1.13bENST0000032384813bENSE00001736813chr1:24981346-24981620275SRRM1_HUMAN347-439930--
1.14aENST0000032384814aENSE00001687798chr1:24987210-2498729081SRRM1_HUMAN439-466280--
1.15aENST0000032384815aENSE00001668356chr1:24987801-2498788787SRRM1_HUMAN466-495300--
1.16aENST0000032384816aENSE00001696627chr1:24989151-24989295145SRRM1_HUMAN495-543490--
1.18bENST0000032384818bENSE00001741254chr1:24993306-24993416111SRRM1_HUMAN543-580380--
1.19bENST0000032384819bENSE00001734803chr1:24995614-24996078465SRRM1_HUMAN580-7351560--
1.19dENST0000032384819dENSE00001616511chr1:24996611-24996806196SRRM1_HUMAN735-800660--
1.20cENST0000032384820cENSE00001642264chr1:24997877-24998086210SRRM1_HUMAN801-870700--
1.21bENST0000032384821bENSE00001942867chr1:24998673-249997581086SRRM1_HUMAN871-904340--

(-) 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:111
 aligned with SRRM1_HUMAN | Q8IYB3 from UniProtKB/Swiss-Prot  Length:904

    Alignment length:117
                                    27        37        47        57        67        77        87        97       107       117       127       
          SRRM1_HUMAN    18 SNKQKKLLKQLKFAECLEKKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVKNPDSKMMQINLTGFLNGKNAREFMGELWPLLLSAQENIAGIPSAFLELKKEEIKQR 134
               SCOP domains d1      mp1a_ A: Ser/Arg-related nuclear matrix protein srm160                                                        SCOP domains
               CATH domains 1m      p1A00 A:24-134 PWI domain                                                                                     CATH domains
               Pfam domains ---------------------------PWI-1mp1A01 A:45-118                                                      ---------------- Pfam domains
         Sec.struct. author ..------......hhhhhh.......hhhhhhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhh......hhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------PWI  PDB: A:27-126 UniProt: 27-126                                                                  -------- PROSITE
               Transcript 1 Exon 1.5            Exon 1.6a  PDB: A:38-78 UniProt: 38-78   Exon 1.6h  PDB: A:79-134 UniProt: 79-135 [INCOMPLETE]    Transcript 1
                 1mp1 A  24 SH------MQLKFAECLEKKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVKNPDSKMMQINLTGFLNGKNAREFMGELWPLLLSAQENIAGIPSAFLELKKEEIKQR 134
                             |      27        37        47        57        67        77        87        97       107       117       127       
                             |     26                                                                                                            
                            25                                                                                                                   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (SRRM1_HUMAN | Q8IYB3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0006405    RNA export from nucleus    The directed movement of RNA from the nucleus to the cytoplasm.
    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:0031124    mRNA 3'-end processing    Any process involved in forming the mature 3' end of an mRNA molecule.
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    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:0006369    termination of RNA polymerase II transcription    The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
cellular component
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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.
    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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