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(-) Description

Authors :  M. Yoneyama, T. Kigawa, N. Tochio, N. Nameki, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 Dec 05  (Deposition) - 15 Jun 06  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Plus-3 Domain; Structural Genomics, Kiaa0252, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  M. Yoneyama, T. Kigawa, N. Tochio, N. Nameki, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The Plus-3 Domain Of Human Kiaa0252 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050302-16
    Expression System Vector TypePLASMID
    FragmentPLUS-3 DOMAIN, RESIDUES 8-143
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymKIAA0252 PROTEIN

 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 2DB9)

(-) Sites  (0, 0)

(no "Site" information available for 2DB9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DB9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DB9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DB9)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
1PLUS3PS51360 Plus3 domain profile.RTF1_HUMAN353-484  1A:14-143

(-) Exons   (6, 6)

NMR Structure (6, 6)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) 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:149
 aligned with RTF1_HUMAN | Q92541 from UniProtKB/Swiss-Prot  Length:710

    Alignment length:181
                                   339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509 
               SCOP domains -----------------d2db9a1 A:8-143 RNA polymerase-associated protein RTF1 homolog                                                                          ---------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------PLUS3  PDB: A:14-143 UniProt: 353-484                                                                                               -------------------------- PROSITE
           Transcript 1 (1) Exon 1.8     -----------------------------------------------------------Exon 1.10b  PDB: A:63-90    -----------------------------Exon 1.12  PDB: A:120-144           Exon 1.13        Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.9  PDB: A:8-62 UniProt: 342-401 [INCOMPLETE]         ---------------------------Exon 1.11  PDB: A:90-119      ---------------------------------------------------- Transcript 1 (2)
                                  |  -       |10        20        30        40        50        60        70        80        90       100       110       120       130       140   |     -         -      |148 
                                  7          8                                                                                                                                     144                    145    

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  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 2DB9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DB9)

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (RTF1_HUMAN | Q92541)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic 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.
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0001832    blastocyst growth    An increase in size of a blastocyst due to expansion of the blastocoelic cavity cell shape changes and cell proliferation.
    GO:0001711    endodermal cell fate commitment    The cell differentiation process that results in commitment of a cell to become part of the endoderm.
    GO:0080182    histone H3-K4 trimethylation    The modification of histone H3 by addition of three methyl groups to lysine at position 4 of the histone.
    GO:0016570    histone modification    The covalent alteration of one or more amino acid residues within a histone protein.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0051571    positive regulation of histone H3-K4 methylation    Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
    GO:0032968    positive regulation of transcription elongation from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0019827    stem cell population maintenance    The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.
    GO:0006368    transcription elongation from RNA polymerase II promoter    The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0016593    Cdc73/Paf1 complex    A multiprotein complex that associates with RNA polymerase II and general RNA polymerase II transcription factor complexes and may be involved in both transcriptional initiation and elongation. In Saccharomyces the complex contains Paf1p, Cdc73p, Ctr9p, Rtf1p, and Leo1p.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

        RTF1_HUMAN | Q925412bze 3u1u 4l1p 4l1u

(-) Related Entries Specified in the PDB File

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