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(-) Description

Title :  SOLUTION STRUCTURE OF THE RNA RECOGNITION MOTIF IN KIAA0430 PROTEIN
 
Authors :  C. Abe, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  16 Mar 06  (Deposition) - 16 Sep 06  (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, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Abe, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The Rna Recognition Motif In Kiaa0430 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KIAA0430 PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050822-19
    Expression System Vector TypePLASMID
    FragmentRNA RECOGNITION MOTIF
    GeneKIAA0430
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-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 2DGX)

(-) Sites  (0, 0)

(no "Site" information available for 2DGX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.MARF1_HUMAN791-870  1A:555-634
2HTH_OSTPS51644 OST-type HTH domain profile.MARF1_HUMAN875-949
1003-1079
1099-1173
1175-1250
1259-1334
1335-1410
1486-1560
1411-1485
  1A:637-641
-
-
-
-
-
-
-

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003963681aENSE00001895064chr16:15737023-15736875149MARF1_HUMAN-00--
1.2ENST000003963682ENSE00002145342chr16:15733148-15732947202MARF1_HUMAN1-48480--
1.3ENST000003963683ENSE00001633385chr16:15730199-15729513687MARF1_HUMAN49-2772290--
1.4ENST000003963684ENSE00001371487chr16:15728788-15728614175MARF1_HUMAN278-336590--
1.5ENST000003963685ENSE00001366932chr16:15727700-15727474227MARF1_HUMAN336-411760--
1.6ENST000003963686ENSE00001156056chr16:15725355-15725238118MARF1_HUMAN412-451400--
1.7ENST000003963687ENSE00001281717chr16:15724361-15724189173MARF1_HUMAN451-508580--
1.8bENST000003963688bENSE00001335517chr16:15719657-15719229429MARF1_HUMAN509-6511430--
1.9ENST000003963689ENSE00001106593chr16:15719030-15718873158MARF1_HUMAN652-704530--
1.10aENST0000039636810aENSE00001156036chr16:15718784-15718626159MARF1_HUMAN704-757540--
1.11aENST0000039636811aENSE00001524729chr16:15716980-15716791190MARF1_HUMAN757-820641A:546-584 (gaps)45
1.12ENST0000039636812ENSE00001389413chr16:15715768-15715590179MARF1_HUMAN821-880601A:585-63652
1.13ENST0000039636813ENSE00001155857chr16:15714388-1571430881MARF1_HUMAN880-907280--
1.14ENST0000039636814ENSE00001391511chr16:15711392-15711156237MARF1_HUMAN907-986801A:637-641 (gaps)18
1.15bENST0000039636815bENSE00001155851chr16:15711028-15710909120MARF1_HUMAN986-1026410--
1.16ENST0000039636816ENSE00001155903chr16:15709862-15709687176MARF1_HUMAN1026-1085600--
1.17bENST0000039636817bENSE00001155899chr16:15706634-15706414221MARF1_HUMAN1085-1158740--
1.18ENST0000039636818ENSE00001391758chr16:15705591-15705449143MARF1_HUMAN1159-1206480--
1.19ENST0000039636819ENSE00001155892chr16:15704965-15704832134MARF1_HUMAN1206-1251460--
1.20ENST0000039636820ENSE00001155887chr16:15703582-15703380203MARF1_HUMAN1251-1318680--
1.21ENST0000039636821ENSE00001106595chr16:15702375-15702148228MARF1_HUMAN1319-1394760--
1.22ENST0000039636822ENSE00001106589chr16:15698255-15698025231MARF1_HUMAN1395-1471770--
1.24ENST0000039636824ENSE00001281756chr16:15696060-15695848213MARF1_HUMAN1472-1542710--
1.26ENST0000039636826ENSE00001106563chr16:15694558-1569449861MARF1_HUMAN1543-1563210--
1.27ENST0000039636827ENSE00001155871chr16:15694410-15694285126MARF1_HUMAN1563-1605430--
1.28ENST0000039636828ENSE00001155865chr16:15692881-15692711171MARF1_HUMAN1605-1662580--
1.29bENST0000039636829bENSE00001950037chr16:15690794-156882442551MARF1_HUMAN1662-1742810--

(-) 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 MARF1_HUMAN | Q9Y4F3 from UniProtKB/Swiss-Prot  Length:1742

    Alignment length:174
                                   785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945    
          MARF1_HUMAN   776 NSSSEADCPDPFANGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGAASKSLSLLSAETMSVLQDAPACCLPLFKFTDIYEKKFGHKLNVSDLYKLTDTVAIREQGNGRLVCLLPSSQARQSPLG 949
               SCOP domains -----------------------d2dgxa1 A:563-635 Limkain-b1, LKAP                                       ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......------...eeeeee......hhhhhhhhhhhhhhhhh.eeeeee.........eeeee.hhhhhhhhhhhhh.eee..eeeeeee.....-----------------------------------------------------------.------...-------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------RRM  PDB: A:555-634 UniProt: 791-870                                            ----HTH_OST  PDB: A:637-641 UniProt: 875-949                                    PROSITE
           Transcript 1 (1) Exon 1.11a  PDB: A:546-584 (gaps)            Exon 1.12  PDB: A:585-636 UniProt: 821-880 [INCOMPLETE]     --------------------------Exon 1.14  PDB: A:637-641 (gaps)            Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------Exon 1.13  PDB: -           ------------------------------------------ Transcript 1 (2)
                 2dgx A 546 GSSGSS------GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGAS-----------------------------------------------------------G------PSS-------G 641
                                 |   -  |    559       569       579       589       599       609       619       629      |  -         -         -         -         -         -      |  -   | |   -   |
                               551    552                                                                                 636                                                         637    638 |     641
                                                                                                                                                                                               640        

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (MARF1_HUMAN | Q9Y4F3)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0006302    double-strand break repair    The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
    GO:0007143    female meiotic nuclear division    A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline.
    GO:0051321    meiotic cell cycle    Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
    GO:0010923    negative regulation of phosphatase activity    Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0048477    oogenesis    The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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