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(-) Description

Title :  SOLUTION STRUCTURE OF THE HOMEOBOX DOMAIN OF HOMEOBOX PROTEIN GOOSECOID
 
Authors :  S. Ohnishi, M. Sato, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  24 Apr 06  (Deposition) - 24 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Homeobox Domain, Three Helices With The Dna Binding Helix- Turn-Helix Motif, Structural Genomics, 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, M. Sato, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Homeobox Domain Of Homeobox Protein Goosecoid
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOMEOBOX PROTEIN GOOSECOID
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050919-23
    Expression System Vector TypePLASMID
    FragmentHOMEOBOX DOMAIN
    GeneGSC
    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 2DMU)

(-) Sites  (0, 0)

(no "Site" information available for 2DMU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_2PS50071 'Homeobox' domain profile.GSC_HUMAN158-218  1A:8-64
2HOMEOBOX_1PS00027 'Homeobox' domain signature.GSC_HUMAN193-216  1A:40-63

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002385581ENSE00001302494chr14:95236499-95235998502GSC_HUMAN1-1191191A:1-7 (gaps)31
1.2ENST000002385582ENSE00001011272chr14:95235554-95235295260GSC_HUMAN119-205871A:8-5245
1.3ENST000002385583ENSE00001306055chr14:95234986-95234561426GSC_HUMAN206-257521A:53-7018

(-) 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 GSC_HUMAN | P56915 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:179
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214         
            GSC_HUMAN    45 GASGGASSDYGAFYPRPVAPGGAGLPAAVSGSRLGYNNYFYGQLHVQAAPVGPACCGAVPPLGAQQCSCVPTPPGYEGPGSVLVSPVPHQMLPYMNVGTLSRTELQLLNQLHCRRKRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRQKRSSS 223
               SCOP domains d2dmu                        a_                                                                                      A: automated matches                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....------------------------..-------------------------------------------------------------------------------------.......hhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------HOMEOBOX_2  PDB: A:8-64 UniProt: 158-218                     ----- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------HOMEOBOX_1  PDB: A:40-63------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:1-7 (gaps) UniProt: 1-119 [INCOMPLETE]                    --------------------------------------------------------------------------------------Exon 1.3           Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------Exon 1.2  PDB: A:8-52 UniProt: 119-205 [INCOMPLETE]                                    ------------------ Transcript 1 (2)
                 2dmu A   1 GSSGS------------------------SG-------------------------------------------------------------------------------------RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGPSSG  70
                                |    -         -         6|        -         -         -         -         -         -         -         -      | 11        21        31        41        51        61         
                                5                        6|                                                                                     8                                                              
                                                          7                                                                                                                                                    

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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 2DMU)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (GSC_HUMAN | P56915)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001103    RNA polymerase II repressing transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription.
    GO:0001085    RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
    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:0009653    anatomical structure morphogenesis    The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
    GO:0021904    dorsal/ventral neural tube patterning    The process in which the neural tube is regionalized in the dorsoventral axis.
    GO:0043583    ear development    The process whose specific outcome is the progression of the ear over time, from its formation to the mature structure. The ear is the sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.
    GO:0048704    embryonic skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized during the embryonic phase.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0007369    gastrulation    A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
    GO:0042474    middle ear morphogenesis    The process in which the anatomical structures of the middle ear are generated and organized. The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window).
    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:0048644    muscle organ morphogenesis    The process in which the anatomical structures of muscle are generated and organized.
    GO:0030178    negative regulation of Wnt signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway.
    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:0014036    neural crest cell fate specification    The process in which a cell becomes capable of differentiating autonomously into a neural crest cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0023019    signal transduction involved in regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another.
cellular component
    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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