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(-) Description

Title :  SOLUTION STRUCTURE OF THE HYPOTHETICAL DOMAIN OF RIKEN CDNA 0610009H20
 
Authors :  R. Hatta, F. Hayashi, M. Yoshida, 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 :  Winged Helix, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Hatta, F. Hayashi, M. Yoshida, S. Yokoyama
Solution Structure Of The Hypothetical Domain Of Riken Cdna 0610009H20
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN (RIKEN CDNA 0610009H20)
    ChainsA
    EngineeredYES
    Expression System PlasmidP030811-04
    Expression System Vector TypePLASMID
    FragmentHYPOTHETICAL DOMAIN
    GeneFANTOM 2 CDNA 0610009H20
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    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 1WJ5)

(-) Sites  (0, 0)

(no "Site" information available for 1WJ5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WJ5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WJ5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WJ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WJ5)

(-) Exons   (0, 0)

(no "Exon" information available for 1WJ5)

(-) 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:120
 aligned with STN1_MOUSE | Q8K2X3 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:228
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323        
           STN1_MOUSE   104 SSSDPAILSTARELSMTSQLKKLQETIEQKTRIGIGDIIRVRGSVRMFREEREICANIYYKVDDPVWNMQIARMLELPKLYQKVYDQPFRNPALQEEEALNNKDNLDLAGLTSLLSEKIKEFLQEKKMQSFYQQELETVESLQSLASRPVTHSTGSDQVELKDSGTSGVAQRVFKNALQLLQEKGLVFQRDSGSDKLYYVTTKDKDLQQKIYHIIKEDCQKPNHMEKG 331
               SCOP domains d1wj5a                                                                                              _ A: OB fold-containing protein 1, Obfc1                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------DUF1879-1wj5A01 A:8-114                                                                                    -------------------- Pfam domains
         Sec.struct. author ......----------------------------------------------------------------------------------------------......hhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhh.ee..........ee.........-----------..---... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wj5 A   1 GSSGSS----------------------------------------------------------------------------------------------GNKDNLDLAGLTSLLSEKIKEFLQEKKMQSFYQQELETVESLQSLASRPVTHSTGSDQVELKDSGTSGVAQRVFKNALQLLQEKGLVFQRDSGSDKLYYVTTKDKDLQS-----------GP---SSG 120
                                 |   -         -         -         -         -         -         -         -         -         -|       16        26        36        46        56        66        76        86        96       106        |-         -||   |  
                                 6                                                                                              7                                                                                                         115         116| 118  
                                                                                                                                                                                                                                                       117      

   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 1WJ5)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (24, 24)

NMR Structure(hide GO term definitions)
Chain A   (STN1_MOUSE | Q8K2X3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    GO:0043047    single-stranded telomeric DNA binding    Interacting selectively and non-covalently with single-stranded telomere-associated DNA.
    GO:0010521    telomerase inhibitor activity    Stops, prevents or reduces the activity of a telomerase. Telomerase catalyzes the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes extension of the 3'- end of a DNA strand by one deoxynucleotide at a time using an internal RNA template that encodes the telomeric repeat sequence.
    GO:0042162    telomeric DNA binding    Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
biological process
    GO:0051974    negative regulation of telomerase activity    Any process that stops or reduces the activity of the enzyme telomerase, which catalyzes of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    GO:0045740    positive regulation of DNA replication    Any process that activates or increases the frequency, rate or extent of DNA replication.
    GO:0051973    positive regulation of telomerase activity    Any process that activates or increases the frequency, rate or extent of telomerase activity, the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    GO:0032212    positive regulation of telomere maintenance via telomerase    Any process that activates or increases the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    GO:1904356    regulation of telomere maintenance via telomere lengthening    Any process that modulates the frequency, rate or extent of telomere maintenance via telomere lengthening.
    GO:0016233    telomere capping    A process in which telomeres are protected from degradation and fusion, thereby ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. May be mediated by specific single- or double-stranded telomeric DNA binding proteins.
    GO:0000723    telomere maintenance    Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
    GO:0010833    telomere maintenance via telomere lengthening    Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins and lengthening the telomeric DNA.
cellular component
    GO:1990879    CST complex    A complex formed by the association of Cdc13 (CTC1 in mammals) with Stn1 in yeast (OBFC1 in mammals) and Ten1 protein (also TEN1 in mammals) with single-stranded telomeric DNA. The CST complex plays a role in telomere protection.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0045111    intermediate filament cytoskeleton    Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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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