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(-) Description

Title :  SOLUTION STRUCTURE OF THE FORKHEAD DOMAIN OF THE ADIPOCYTE-TRANSCRIPTION FACTOR FREAC-11 (S12)
 
Authors :  M. J. P. Van Dongen, A. Cederberg, P. Carlsson, S. Enerback, M. Wikstrom
Date :  12 Oct 99  (Deposition) - 11 Oct 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (25x)
Keywords :  Winged Helix, Dna-Recognition Helix, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Van Dongen, A. Cederberg, P. Carlsson, S. Enerback, M. Wikstrom
Solution Structure And Dynamics Of The Dna-Binding Domain Of The Adipocyte-Transcription Factor Freac-11.
J. Mol. Biol. V. 296 351 2000
PubMed-ID: 10669593  |  Reference-DOI: 10.1006/JMBI.1999.3476
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - S12 TRANSCRIPTION FACTOR (FKH-14)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-11A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentDNA-BINDING DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    TissueADIPOSE TISSUE

 Structural Features

(-) Chains, Units

  
NMR Structure (25x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1D5V)

(-) Sites  (0, 0)

(no "Site" information available for 1D5V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D5V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1D5V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018418S125LFOXC2_HUMANDisease (LYD)121909106AS57L

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

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FORK_HEAD_1PS00657 Fork head domain signature 1.FOXC2_HUMAN72-85  1A:4-17
2FORK_HEAD_3PS50039 Fork head domain profile.FOXC2_HUMAN72-166  1A:4-94
3FORK_HEAD_2PS00658 Fork head domain signature 2.FOXC2_HUMAN116-122  1A:48-54

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003203541ENSE00001280565chr16:86600857-866025391683FOXC2_HUMAN1-5305301A:1-94 (gaps)129

(-) 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:94
 aligned with FOXC2_HUMAN | Q99958 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:129
                                    43        53        63        73        83        93       103       113       123       133       143       153         
          FOXC2_HUMAN    34 MASPMGVYSGHPEQYSAGMGRSYAPYHHHQPAAPKDLVKPPYSYIALITMAIQNAPEKKITLNGIYQFIMDRFPFYRENKQGWQNSIRHNLSLNECFVKVPRDDKKPGKGSYWTLDPDSYNMFENGSFL 162
               SCOP domains d                                   1d5va_ A: Adipocyte-transcription factor FREAC-11 (s12, fkh-14)                               SCOP domains
               CATH domains 1                                   d5vA00 A:1-94 'winged helix' repressor DNA binding domain                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----------------------------------......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..eee.............eee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------L------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------FORK_HEAD_1   ------------------------------FORK_HE---------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------FORK_HEAD_3  PDB: A:4-94 UniProt: 72-166                                                    PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:1-94 (gaps) UniProt: 1-530 [INCOMPLETE]                                                                          Transcript 1
                 1d5v A   1 M-----------------------------------LVKPPYSYIALITMAIQNAPEKKITLNGIYQFIMDRFPFYRENKQGWQNSIRHNLSLNECFVKVPRDDKKPGKGSYWTLDPDSYNMFENGSFL  94
                            |        -         -         -      |  5        15        25        35        45        55        65        75        85         
                            |                                   2                                                                                            
                            1                                                                                                                                

   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  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D5V)

(-) Gene Ontology  (58, 58)

NMR Structure(hide GO term definitions)
Chain A   (FOXC2_HUMAN | Q99958)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0031490    chromatin DNA binding    Interacting selectively and non-covalently with DNA that is assembled into chromatin.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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: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: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: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:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter 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:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0048844    artery morphogenesis    The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs.
    GO:0001568    blood vessel development    The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.
    GO:0001974    blood vessel remodeling    The reorganization or renovation of existing blood vessels.
    GO:0001569    branching involved in blood vessel morphogenesis    The process of coordinated growth and sprouting of blood vessels giving rise to the organized vascular system.
    GO:0043010    camera-type eye development    The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
    GO:0060038    cardiac muscle cell proliferation    The expansion of a cardiac muscle cell population by cell division.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0030199    collagen fibril organization    Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix.
    GO:0048701    embryonic cranial skeleton morphogenesis    The process in which the anatomical structures of the cranial skeleton 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:0048704    embryonic skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized during the embryonic phase.
    GO:0048703    embryonic viscerocranium morphogenesis    The process in which the anatomical structures of the viscerocranium are generated and organized during the embryonic phase. The viscerocranium is the part of the skull comprising the facial bones.
    GO:0072011    glomerular endothelium development    The process whose specific outcome is the progression of the glomerular endothelium over time, from its formation to the mature structure. The glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus.
    GO:0072144    glomerular mesangial cell development    The process whose specific outcome is the progression of a glomerular mesangial cell in the kidney over time, from its formation to the mature structure.
    GO:0072112    glomerular visceral epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a glomerular visceral epithelial cell. A glomerular visceral epithelial cell is a specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0001945    lymph vessel development    The process whose specific outcome is the progression of a lymph vessel over time, from its formation to the mature structure.
    GO:0001946    lymphangiogenesis    Lymph vessel formation when new vessels emerge from the proliferation of pre-existing vessels.
    GO:0007498    mesoderm development    The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue.
    GO:0001656    metanephros development    The process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine.
    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:1902257    negative regulation of apoptotic process involved in outflow tract morphogenesis    Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis.
    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:0014032    neural crest cell development    The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
    GO:0001503    ossification    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0048341    paraxial mesoderm formation    The process that gives rise to the paraxial mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
    GO:0048343    paraxial mesodermal cell fate commitment    The process in which a cell becomes committed to become a paraxial mesoderm cell.
    GO:0033630    positive regulation of cell adhesion mediated by integrin    Any process that activates or increases the frequency, rate, or extent of cell adhesion mediated by integrin.
    GO:0090050    positive regulation of cell migration involved in sprouting angiogenesis    Any process that increases the frequency, rate or extent of cell migration involved in sprouting angiogenesis. Cell migration involved in sprouting angiogenesis is the orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels contributing to the process of sprouting angiogenesis.
    GO:0010595    positive regulation of endothelial cell migration    Any process that increases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    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:0035470    positive regulation of vascular wound healing    Any process that increases the rate, frequency, or extent of blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to damaged vasculature.
    GO:0050880    regulation of blood vessel size    Any process that modulates the size of blood vessels.
    GO:0046620    regulation of organ growth    Any process that modulates the frequency, rate or extent of growth of an organ of an organism.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009725    response to hormone    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 hormone stimulus.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
    GO:0001756    somitogenesis    The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001657    ureteric bud development    The process whose specific outcome is the progression of the ureteric bud over time, from its formation to the mature structure.
    GO:0048010    vascular endothelial growth factor receptor signaling pathway    Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0055010    ventricular cardiac muscle tissue morphogenesis    The process in which the anatomical structures of cardiac ventricle muscle is generated and organized.
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.

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