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(-) Description

Title :  SOLUTION STRUCTURE OF THE 4TH HMG-BOX OF MOUSE UBF1
 
Authors :  K. Saito, S. Koshiba, M. Inoue, T. Kigawa, 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 :  Transcription Factor, Dna Binding, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Saito, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The 4Th Hmg-Box Of Mouse Ubf1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UPSTREAM BINDING FACTOR 1
    ChainsA
    EngineeredYES
    Expression System PlasmidP031117-29
    Expression System Vector TypePLASMID
    FragmentHMG BOX DOMAIN
    GeneRIKEN CDNA 1300010N03
    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 1WGF)

(-) Sites  (0, 0)

(no "Site" information available for 1WGF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.UBF1_MOUSE112-180
196-264
407-475
298-362
482-549
568-634
  2-
-
A:21-86
-
A:87-90
-

(-) Exons   (0, 0)

(no "Exon" information available for 1WGF)

(-) 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:90
 aligned with UBF1_MOUSE | P25976 from UniProtKB/Swiss-Prot  Length:765

    Alignment length:124
                                   384       394       404       414       424       434       444       454       464       474       484       494    
           UBF1_MOUSE   375 GEEKMLNINKKQTTSPASKKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLTEKKKAKYKAREAALKAQSERKPGGEREDRGKLPESPKRAEEIWQQSVIG 498
               SCOP domains d            1wgfa_ A: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------HMG_box-1wgfA01 A:21-84                                         ---------------------------- Pfam domains
         Sec.struct. author .------------........................hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........---------...-------------. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------HMG_BOX_2  PDB: A:21-86 UniProt: 407-475                             ------HMG_BOX_2         PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wgf A   1 G------------SSGSSGKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSG---------PSS-------------G  90
                            |        -   |     8        18        28        38        48        58        68        78       | -       |89         -   |
                            |            2                                                                                  86        87 |            90
                            1                                                                                                           89              

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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  (0, 0)

(no "CATH Domain" information available for 1WGF)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HMG-box (15)

(-) Gene Ontology  (11, 11)

NMR Structure(hide GO term definitions)
Chain A   (UBF1_MOUSE | P25976)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001164    RNA polymerase I CORE element sequence-specific DNA binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery. This site is often referred to as the CORE element. In mammalian cells, the CORE element functions in conjunction with the Upstream Control Element (UCE), while in fungi, protozoa, and plants, the CORE element functions without a UCE.
    GO:0001165    RNA polymerase I upstream control element sequence-specific DNA binding    Interacting selectively and non-covalently with the upstream control element (UCE, or alternately referred to as the upstream element), a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase I.
    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:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0045943    positive regulation of transcription from RNA polymerase I promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase I promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006362    transcription elongation from RNA polymerase I promoter    The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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: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)

UniProtKB/Swiss-Prot
        UBF1_MOUSE | P259761v63 1v64

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