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(-) Description

Title :  SOLUTION STRUCTURE OF THE HOMEOBOX DOMAIN OF THE HUMAN HYPOTHETICAL PROTEIN FLJ21616
 
Authors :  S. Ohnishi, T. Kigawa, T. Tomizawa, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 May 05  (Deposition) - 26 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Homeobox Domain, Flj21616, Hepatocyte Transcription Factor, Structural Genomics, Loop Insertion, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Ohnishi, T. Kigawa, T. Tomizawa, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The Homeobox Domain Of The Human Hypothetical Protein Flj21616
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FLJ21616 PROTEIN
    ChainsA
    EngineeredYES
    Expression System PlasmidP041004-01
    Expression System Vector TypePLASMID
    FragmentHOMEOBOX DOMAIN
    GeneFLJ21616
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    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 2CUF)

(-) Sites  (0, 0)

(no "Site" information available for 2CUF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_2PS50071 'Homeobox' domain profile.HMBX1_HUMAN265-340  1A:8-80

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003973582ENSE00001528410chr8:28748225-28748536312HMBX1_HUMAN-00--
1.3ENST000003973583ENSE00001528408chr8:28749277-2874930731HMBX1_HUMAN-00--
1.5aENST000003973585aENSE00002194913chr8:28821328-2882140780HMBX1_HUMAN1-880--
1.6bENST000003973586bENSE00001410929chr8:28827560-28828036477HMBX1_HUMAN8-1671600--
1.7ENST000003973587ENSE00000980045chr8:28837588-2883767386HMBX1_HUMAN167-196300--
1.8ENST000003973588ENSE00000980046chr8:28866589-28866699111HMBX1_HUMAN196-233381A:1-22
1.10bENST0000039735810bENSE00001030031chr8:28876277-28876430154HMBX1_HUMAN233-284521A:3-24 (gaps)27
1.12ENST0000039735812ENSE00001030034chr8:28902878-2890296083HMBX1_HUMAN284-312291A:24-5229
1.14ENST0000039735814ENSE00001030028chr8:28904875-2890497096HMBX1_HUMAN312-344331A:52-8332
1.15aENST0000039735815aENSE00001030026chr8:28906471-2890656595HMBX1_HUMAN344-375321A:84-95 (gaps)15
1.17hENST0000039735817hENSE00001528397chr8:28908535-289107872253HMBX1_HUMAN376-420450--

(-) 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:95
 aligned with HMBX1_HUMAN | Q6NT76 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:150
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359
          HMBX1_HUMAN   210 GSDLSEQKKRAFYRWYQLEKTNPGATLSMRPAPIPIEDPEWRQTPPPVSATSGTFRLRRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIEAAILESHGIDVQSPG 359
               SCOP domains ----------------------------------------------------------d2cufa1 A:8-89 Homeobox-containing protein 1, HMBOX1 (Flj21616)                    --------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..----------------------------------------------.....-----........hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh.-........---.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------HOMEOBOX_2  PDB: A:8-80 UniProt: 265-340                                    ------------------- PROSITE
           Transcript 1 (1) -----------------------Exon 1.10b  PDB: A:3-24 (gaps) UniProt: 233-284     ---------------------------Exon 1.14  PDB: A:52-83          --------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.8  PDB: A:1-2    --------------------------------------------------Exon 1.12  PDB: A:24-52      -------------------------------Exon 1.15a       Transcript 1 (2)
                 2cuf A   1 GS----------------------------------------------SGSSG-----RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI-AAILESSG---PSSG  95
                             |       -         -         -         -        |4  |     |9        19        29        39        49        59        69        79   | |  88  |   | 95
                             2                                              3   7     8                                                                         83 |     91  92   
                                                                                                                                                                  84              

   Legend:   → Mismatch (orange background)
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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 2CUF)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (HMBX1_HUMAN | Q6NT76)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003691    double-stranded telomeric DNA binding    Interacting selectively and non-covalently with double-stranded telomere-associated DNA.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003720    telomerase activity    Catalysis of 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:0006278    RNA-dependent DNA biosynthetic process    A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0035563    positive regulation of chromatin binding    Any process that increases the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    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.
    GO:0005697    telomerase holoenzyme complex    Telomerase is a ribonucleoprotein enzyme complex, with a minimal catalytic core composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition. In vivo, the holoenzyme complex often contains additional subunits.

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        HMBX1_HUMAN | Q6NT764j19

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