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(-) Description

Authors :  K. Seimiya, F. Hayashi, T. Nagashima, M. Yoshida, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  20 May 05  (Deposition) - 20 Nov 05  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Dna-Binding, Transcription Regulation, Helix-Turn-Helix, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  K. Seimiya, F. Hayashi, T. Nagashima, M. Yoshida, S. Yokoyama
Solution Structure Of The Homeobox Domain Of Human Homeo Box B13
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

    Expression System PlasmidP040607-07
    Expression System Vector TypePLASMID
    FragmentHOMEOBOX (RESIDUES 1-70)
    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 2CRA)

(-) Sites  (0, 0)

(no "Site" information available for 2CRA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

NMR Structure (3, 3)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
3UniProtVAR_071870R229GHXB13_HUMANUnclassified  ---AR20G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
1HOMEOBOX_2PS50071 'Homeobox' domain profile.HXB13_HUMAN214-274  1A:7-63
2HOMEOBOX_1PS00027 'Homeobox' domain signature.HXB13_HUMAN249-272  1A:40-63

(-) Exons   (2, 2)

NMR Structure (2, 2)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000002902952ENSE00001043851chr17:46804405-468021252281HXB13_HUMAN201-284841A:1-70 (gaps)83

(-) 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:70
 aligned with HXB13_HUMAN | Q92826 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:83
                                   210       220       230       240       250       260       270       280   
               SCOP domains ---------------d2craa1 A:7-64 Homeobox protein hox-b13                       ------ SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......---------........hhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhh..----....... Sec.struct. author
                 SAPs(SNPs) ---------------CC-----------G------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------HOMEOBOX_2  PDB: A:7-63 UniProt: 214-274                     --------- PROSITE (1)
                PROSITE (2) ------------------------------------------------HOMEOBOX_1  PDB: A:40-63----------- PROSITE (2)
           Transcript 1 (1) 1---------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.2  PDB: A:1-70 (gaps) UniProt: 201-284 [INCOMPLETE]                          Transcript 1 (2)
                                 |   -     |  11        21        31        41        51        61 |    | 67   
                                 6         7                                                      63   64      

   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 2CRA)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (HXB13_HUMAN | Q92826)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0008544    epidermis development    The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
    GO:0060743    epithelial cell maturation involved in prostate gland development    The developmental process, independent of morphogenetic (shape) change, that is required for an epithelial cell of the prostate gland to attain its fully functional state. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface.
    GO:0002009    morphogenesis of an epithelium    The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0060527    prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis    The branching morphogenesis process in which the prostate epithelial cords branch freely to create the structure of the prostate acini.
    GO:0040008    regulation of growth    Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0033574    response to testosterone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus.
    GO:0009611    response to wounding    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.


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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

        HXB13_HUMAN | Q928265edn 5eea 5ef6 5eg0 5ego

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