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(-) Description

Authors :  Y. Xu, W. Yang, J. Wu, Y. Shi
Date :  28 Oct 01  (Deposition) - 14 Nov 01  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Alpha-Helix, L-Shape, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  Y. Xu, W. Yang, J. Wu, Y. Shi
Solution Structure Of The First Hmg Box Domain In Human Upstream Binding Factor.
Biochemistry V. 41 5415 2002
PubMed-ID: 11969401  |  Reference-DOI: 10.1021/BI015977A
(for further references see the PDB file header)

(-) Compounds

    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET-22B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentHMG BOX 1
    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 1K99)

(-) Sites  (0, 0)

(no "Site" information available for 1K99)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K99)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K99)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K99)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.UBF1_HUMAN112-180

(-) Exons   (4, 4)

NMR Structure (4, 4)
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:91
 aligned with UBF1_HUMAN | P17480 from UniProtKB/Swiss-Prot  Length:764

    Alignment length:91
                                   111       121       131       141       151       161       171       181       191 
               SCOP domains d1k99a_ A: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)              SCOP domains
               CATH domains 1k99A00 A:1-91 DNA Binding (I), subunit A                                                   CATH domains
               Pfam domains ----------HMG_box-1k99A01 A:11-79                                              ------------ Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------HMG_BOX_2  PDB: A:11-79 UniProt: 112-180                             ------------ PROSITE
           Transcript 1 (1) 1.7  Exon 1.8  PDB: A:6-57 UniProt: 107-158              ---------------------Exon 1.10     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.9c  PDB: A:58-7------------ Transcript 1 (2)
                                    10        20        30        40        50        60        70        80        90 

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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  (1, 1)

NMR Structure

(-) Pfam Domains  (1, 1)

NMR Structure
Clan: HMG-box (15)

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (UBF1_HUMAN | P17480)
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: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:1902659    regulation of glucose mediated signaling pathway    Any process that modulates the frequency, rate or extent of glucose mediated signaling pathway.
    GO:0006356    regulation of transcription from RNA polymerase I promoter    Any process that modulates 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:0006363    termination of RNA polymerase I transcription    The process in which the synthesis of an RNA molecule by RNA polymerase I using a DNA template is completed. RNAP I termination requires binding of a terminator protein so specific sequences downstream of the transcription unit.
    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:0006360    transcription from RNA polymerase I promoter    The synthesis of RNA from a DNA template by RNA polymerase I (RNAP I), originating at an RNAP I promoter.
    GO:0006361    transcription initiation from RNA polymerase I promoter    Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an RNA polymerase I promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0001650    fibrillar center    A structure found most metazoan nucleoli, but not usually found in lower eukaryotes; surrounded by the dense fibrillar component; the zone of transcription from multiple copies of the pre-rRNA genes is in the border region between these two structures.
    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)

        UBF1_HUMAN | P174801l8y 1l8z 2hdz

(-) Related Entries Specified in the PDB File

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