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(-) Description

Title :  STRUCTURE OF THE THIRD HOMEODOMAIN FROM THE HUMAN HOMEOBOX AND LEUCINE ZIPPER PROTEIN, HOMEZ
 
Authors :  S. Ohnishi, T. Tomizawa, S. Koshiba, T. Harada, S. Watanabe, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  03 Apr 07  (Deposition) - 09 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Homez, Homeodomain, Nmr, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Ohnishi, T. Tomizawa, S. Koshiba, T. Harada, S. Watanabe, T. Kigawa, S. Yokoyama
Structure Of The Third Homeodomain From The Human Homeobox And Leucine Zipper Protein, Homez
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOMEOBOX AND LEUCINE ZIPPER PROTEIN HOMEZ
    ChainsA
    EngineeredYES
    Expression System PlasmidP051011-14
    Expression System Vector TypePLASMID
    FragmentHOMEODOMAIN
    GeneHOMEZ
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymHOMEODOMAIN LEUCINE ZIPPER-CONTAINING FACTOR

 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 2YS9)

(-) Sites  (0, 0)

(no "Site" information available for 2YS9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YS9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YS9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YS9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YS9)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003574601ENSE00001540690chr14:23755309-23755122188HOMEZ_HUMAN1-14140--
1.2ENST000003574602ENSE00001426232chr14:23746396-237428443553HOMEZ_HUMAN14-5505371A:1-70 (gaps)124

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:70
 aligned with HOMEZ_HUMAN | Q8IX15 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:124
                                   414       424       434       444       454       464       474       484       494       504       514       524    
          HOMEZ_HUMAN   405 GDTRYALKHGQLKWFRDNAVPGAPSFQDPAIPTPPPSTRSLNERAETPPLPIPPPPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSRLPQPAEVVVCLDEEEEEEEEELPEDD 528
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...------------------..-----------------------............hhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhhh........-------------.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: A:1-70 (gaps) UniProt: 14-550 [INCOMPLETE]                                                                    Transcript 1
                 2ys9 A   1 GSS------------------GS-----------------------SGPLPIPPPPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSRLPQPAEVSG-------------PSSG  70
                              |      -         - ||      -         -      |  9        19        29        39        49        59      |  -         -|   
                              3                  4|                       6                                                          66            67   
                                                  5                                                                                                     

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    → 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  (0, 0)

(no "SCOP Domain" information available for 2YS9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YS9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YS9)

(-) Gene Ontology  (10, 10)

NMR Structure(hide GO term definitions)
Chain A   (HOMEZ_HUMAN | Q8IX15)
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:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    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: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: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

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        HOMEZ_HUMAN | Q8IX152ecc

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