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(-) Description

Title :  SOLUTION STRUCTURE OF THE HMG BOX OF HUMAN TRANSCRIPTION FACTOR SOX-17
 
Authors :  H. Abe, N. Tochio, K. Miyamoto, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 Apr 07  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Transcription, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Abe, N. Tochio, K. Miyamoto, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Hmg Box Of Human Transcription Factor Sox-17
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR SOX-17
    ChainsA
    EngineeredYES
    Expression System PlasmidP051003-07
    Expression System Vector TypePLASMID
    FragmentHMG (HIGH MOBILITY GROUP) BOX
    GeneSOX17
    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 2YUL)

(-) Sites  (0, 0)

(no "Site" information available for 2YUL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.SOX17_HUMAN68-136  1A:8-76

(-) Exons   (0, 0)

(no "Exon" information available for 2YUL)

(-) 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:82
 aligned with SOX17_HUMAN | Q9H6I2 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:116
                                    66        76        86        96       106       116       126       136       146       156       166      
          SOX17_HUMAN    57 GAAGRAKGESRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKYRPRRRKQVKRLKRVEGGFLHGLAEPQAAALGPEGG 172
               SCOP domains d2y    ula_ A: automated matches                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------HMG_box-2yulA01 A:8-76                                               ------------------------------------ Pfam domains
         Sec.struct. author ...----.........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......------------------------------..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------HMG_BOX_2  PDB: A:8-76 UniProt: 68-136                               ------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2yul A   1 GSS----GSSGIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKS------------------------------GPSSG  82
                              |    | 6        16        26        36        46        56        66        76|        -         -         - |    
                              3    4                                                                       77                             78    

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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 2YUL)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HMG-box (15)

(-) Gene Ontology  (70, 70)

NMR Structure(hide GO term definitions)
Chain A   (SOX17_HUMAN | Q9H6I2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    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.
    GO:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0003705    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    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.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0001228    transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0060070    canonical Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
    GO:0060913    cardiac cell fate determination    The process involved in cardiac cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.
    GO:0003142    cardiogenic plate morphogenesis    The process in which the anatomical structures of the cardiogenic plate are generated and organized. The cardiogenic plate is the first recognizable structure derived from the heart field.
    GO:0042074    cell migration involved in gastrulation    The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression).
    GO:0061009    common bile duct development    The progression of the common bile duct over time, from its formation to the mature structure. The common bile duct is formed from the joining of the common hepatic duct running from the liver, and the cystic duct running from the gall bladder. The common bile duct transports bile from the liver and gall bladder to the intestine.
    GO:0048617    embryonic foregut morphogenesis    The process in which the anatomical structures of the foregut are generated and organized, during the embryonic phase.
    GO:0035050    embryonic heart tube development    The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field.
    GO:0003143    embryonic heart tube morphogenesis    The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart.
    GO:0048568    embryonic organ development    Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0060956    endocardial cell differentiation    The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an endocardial cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart. The endocardium is the innermost layer of tissue of the heart, and lines the heart chambers.
    GO:0060214    endocardium formation    Formation of the endocardium of the heart. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.
    GO:0007492    endoderm development    The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues.
    GO:0001706    endoderm formation    The formation of the endoderm during gastrulation.
    GO:0007493    endodermal cell fate determination    The cell fate determination process in which a cell becomes capable of differentiating autonomously into an endoderm cell regardless of its environment; upon determination, the cell fate cannot be reversed.
    GO:0061031    endodermal digestive tract morphogenesis    The process in which the anatomical structures of the endodermal digestive tract are generated and organized. The endodermal digestive tract includes those portions of the digestive tract that are derived from endoderm.
    GO:0061010    gall bladder development    The progression of the gall bladder over time, from its initial formation to the mature structure. The gall bladder is a cavitated organ that stores bile.
    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:0060914    heart formation    The developmental process pertaining to the initial formation of the heart from unspecified parts. This process begins with the specific processes that contribute to the appearance of the heart field and the arrival of cardiac neural crest to the heart region. The process ends when the structural rudiment is recognizable.
    GO:0001947    heart looping    The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation.
    GO:0001828    inner cell mass cellular morphogenesis    The morphogenesis of cells in the inner cell mass.
    GO:0042789    mRNA transcription from RNA polymerase II promoter    The cellular synthesis of messenger RNA (mRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter.
    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:0003308    negative regulation of Wnt signaling pathway involved in heart development    Any process that decreases the rate, frequency, or extent of the series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell, resulting a change in cell state that contributes to the progression of the heart over time.
    GO:0090090    negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0042662    negative regulation of mesodermal cell fate specification    Any process that stops, prevents, or reduces the frequency, rate or extent of mesoderm cell fate specification.
    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:0003151    outflow tract morphogenesis    The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries.
    GO:0045597    positive regulation of cell differentiation    Any process that activates or increases the frequency, rate or extent of cell differentiation.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0048643    positive regulation of skeletal muscle tissue development    Any process that activates, maintains or increases the rate of skeletal muscle tissue development.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0031648    protein destabilization    Any process that decreases the stability of a protein, making it more vulnerable to degradative processes or aggregation.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
    GO:2000043    regulation of cardiac cell fate specification    Any process that modulates the frequency, rate or extent of cardiac cell fate specification.
    GO:0045595    regulation of cell differentiation    Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
    GO:0045995    regulation of embryonic development    Any process that modulates the frequency, rate or extent of embryonic development.
    GO:0042661    regulation of mesodermal cell fate specification    Any process that modulates the frequency, rate or extent of mesoderm cell fate specification.
    GO:2000035    regulation of stem cell division    Any process that modulates the frequency, rate or extent of stem cell division.
    GO:0072091    regulation of stem cell proliferation    Any process that modulates the frequency, rate or extent of stem cell proliferation. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
    GO:0060807    regulation of transcription from RNA polymerase II promoter involved in definitive endodermal cell fate specification    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that ultimately results in a cell being specified to adopt a definitive endodermal cell fate.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0072001    renal system development    The process whose specific outcome is the progression of the renal system over time, from its formation to the mature structure. The renal system maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels.
    GO:0021903    rostrocaudal neural tube patterning    The process in which the neural tube is divided into specific regions along the rostrocaudal axis.
    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.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0048863    stem cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
    GO:0048866    stem cell fate specification    The process in which a cell becomes capable of differentiating autonomously into a stem cell in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001570    vasculogenesis    The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes.
cellular component
    GO:0044798    nuclear transcription factor complex    A protein complex, located in the nucleus, that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
    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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