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(-) Description

Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 Apr 06  (Deposition) - 06 Oct 06  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Structural Genomics, Winged Helix Domain, Dna-Directed Rna Polymerase Iii, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Translation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of Winged-Helix Domain In Rna Polymerase Iii 39Kda Polypeptide
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

    EC Number2.7.7.6
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050829-03
    Expression System Vector TypePLASMID
    GenePOLR3F, RPC39
    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 2DK5)

(-) Sites  (0, 0)

(no "Site" information available for 2DK5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DK5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DK5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DK5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DK5)

(-) Exons   (5, 5)

NMR Structure (5, 5)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3aENST000003776033aENSE00000906792chr20:18453486-1845355368RPC6_HUMAN61-83231A:4-13 (gaps)23
1.6ENST000003776036ENSE00000906795chr20:18460682-18460825144RPC6_HUMAN144-191481A:74-91 (gaps)21

(-) 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:91
 aligned with RPC6_HUMAN | Q9H1D9 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:107
                                    67        77        87        97       107       117       127       137       147       157       
               SCOP domains --------------------d2dk5a1 A:8-85 DNA-directed RNA polymerase III subunit RPC6, RPO3F            --------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....-------...------..............hhhhhhhhhhh....eehhhhhhh....hhhhhhhhhhhhh...eeee.........eeee....---..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.2Exon 1.3a              ----------------------Exon 1.5  PDB: A:36-73                Exon 1.6 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.4  PDB: A:13-36  ---------------------------------------------------------- Transcript 1 (2)
                               |     - | |     -|       17        27        37        47        57        67        77        |-  |    
                               4       5 7      8                                                                            86  87    

   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 2DK5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DK5)

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (RPC6_HUMAN | Q9H1D9)
molecular function
    GO:0003899    DNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
    GO:0001056    RNA polymerase III activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase III specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
    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:0032774    RNA biosynthetic process    The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0045089    positive regulation of innate immune response    Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
    GO:0032728    positive regulation of interferon-beta production    Any process that activates or increases the frequency, rate, or extent of interferon-beta production.
    GO:0032481    positive regulation of type I interferon production    Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0006359    regulation of transcription from RNA polymerase III promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA ploymerase III promoter.
    GO:0006383    transcription from RNA polymerase III promoter    The synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter.
cellular component
    GO:0005666    DNA-directed RNA polymerase III complex    RNA polymerase III, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces 5S rRNA, tRNAs and some of the small nuclear RNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase I and others of which are also found in RNA polymerases I and II. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.
    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: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)

        RPC6_HUMAN | Q9H1D92yu3

(-) Related Entries Specified in the PDB File

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