Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  OPPOSITE GATA DNA BINDING
 
Authors :  D. L. Bates, G. K. Kim, L. Guo, L. Chen
Date :  12 Jun 08  (Deposition) - 29 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,X,Y
Keywords :  Activator, Dna-Binding, Metal-Binding, Nucleus, Transcription, Transcription Regulation, Zinc, Zinc-Finger, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. L. Bates, Y. Chen, G. Kim, L. Guo, L. Chen
Crystal Structures Of Multiple Gata Zinc Fingers Bound To Dna Reveal New Insights Into Dna Recognition And Self-Association By Gata.
J. Mol. Biol. V. 381 1292 2008
PubMed-ID: 18621058  |  Reference-DOI: 10.1016/J.JMB.2008.06.072
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANS-ACTING T-CELL-SPECIFIC TRANSCRIPTION FACTOR GATA-3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainROSETTA PLYS
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 308-370
    GeneGATA3, GATA-3
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymGATA-BINDING FACTOR 3
 
Molecule 2 - DNA (5'- D(*DTP*DTP*DGP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DGP*DAP*DGP* DAP*DTP*DAP*DAP*DCP*DC)-3')
    ChainsX
    EngineeredYES
    SyntheticYES
 
Molecule 3 - DNA (5'- D(*DAP*DAP*DGP*DGP*DTP*DTP*DAP*DTP*DCP*DTP*DCP*DTP*DGP*DAP* DTP*DTP*DTP*DAP*DTP*DC)-3')
    ChainsY
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:317 , CYS A:320 , THR A:322 , CYS A:338 , CYS A:341BINDING SITE FOR RESIDUE ZN A 30
2AC2SOFTWARECYS B:317 , CYS B:320 , CYS B:338 , CYS B:341BINDING SITE FOR RESIDUE ZN B 30

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DFX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DFX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DFX)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GATA_ZN_FINGER_2PS50114 GATA-type zinc finger domain profile.GATA3_MOUSE257-311
311-364
 
  2-
A:311-364
B:311-364
2GATA_ZN_FINGER_1PS00344 GATA-type zinc finger domain.GATA3_MOUSE263-287
317-341
 
  2-
A:317-341
B:317-341

(-) Exons   (0, 0)

(no "Exon" information available for 3DFX)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:58
 aligned with GATA3_MOUSE | P23772 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:58
                                   317       327       337       347       357        
          GATA3_MOUSE   308 SAARRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINRPLTMKKEGIQTRN 365
               SCOP domains d3dfxa_ A: automated matches                               SCOP domains
               CATH domains 3dfxA00 A:308-365                                          CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................hhhhhhhhhhhh...hhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) GATA-----GATA_ZN_FINGER_1         ------------------------ PROSITE (1)
                PROSITE (2) ---GATA_ZN_FINGER_2  PDB: A:311-364 UniProt: 311-364     - PROSITE (2)
                 Transcript ---------------------------------------------------------- Transcript
                 3dfx A 308 SAARRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINRPLTMKKEGIQTRN 365
                                   317       327       337       347       357        

Chain B from PDB  Type:PROTEIN  Length:58
 aligned with GATA3_MOUSE | P23772 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:58
                                   317       327       337       347       357        
          GATA3_MOUSE   308 SAARRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINRPLTMKKEGIQTRN 365
               SCOP domains d3dfxb_ B: automated matches                               SCOP domains
               CATH domains 3dfxB00 B:308-365                                          CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .....................ee.....eehhhhhhhhhhhh...hhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) GATA-----GATA_ZN_FINGER_1         ------------------------ PROSITE (1)
                PROSITE (2) ---GATA_ZN_FINGER_2  PDB: B:311-364 UniProt: 311-364     - PROSITE (2)
                 Transcript ---------------------------------------------------------- Transcript
                 3dfx B 308 SAARRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINRPLTMKKEGIQTRN 365
                                   317       327       337       347       357        

Chain X from PDB  Type:DNA  Length:20
                                                    
                 3dfx X   1 TTGATAAATCAGAGATAACC  20
                                    10        20

Chain Y from PDB  Type:DNA  Length:20
                                                    
                 3dfx Y   1 AAGGTTATCTCTGATTTATC  20
                                    10        20

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DFX)

(-) Gene Ontology  (146, 146)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GATA3_MOUSE | P23772)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0070888    E-box binding    Interacting selectively and non-covalently with an E-box, a DNA motif with the consensus sequence CANNTG that is found in the promoters of a wide array of genes expressed in neurons, muscle and other tissues.
    GO:0071837    HMG box domain binding    Interacting selectively and non-covalently with an HMG box domain, a protein domain that consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin.
    GO:0000979    RNA polymerase II core promoter sequence-specific DNA binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    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:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0000987    core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon.
    GO:0001046    core promoter sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region composed of the transcription start site and binding sites for the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon.
    GO:0001158    enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
    GO:0005134    interleukin-2 receptor binding    Interacting selectively and non-covalently with the interleukin-2 receptor.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0001071    nucleic acid binding transcription factor activity    Interacting selectively and non-covalently with a DNA or RNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular 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:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    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: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:0000976    transcription regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
    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.
    GO:0001078    transcriptional repressor 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 stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030217    T cell differentiation    The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
    GO:0033077    T cell differentiation in thymus    The process in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0045064    T-helper 2 cell differentiation    The process in which a relatively unspecialized T cell acquires specialized features of a T-helper 2 (Th2) cell. A Th2 cell is a CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive and produces interleukin-4.
    GO:0031929    TOR signaling    A series of molecular signals mediated by TOR (Target of rapamycin) proteins, members of the phosphoinositide (PI) 3-kinase related kinase (PIKK) family that act as serine/threonine kinases in response to nutrient availability or growth factors.
    GO:0048646    anatomical structure formation involved in morphogenesis    The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
    GO:0003180    aortic valve morphogenesis    The process in which the structure of the aortic valve is generated and organized.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0061290    canonical Wnt signaling pathway involved in metanephric kidney development    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 that contribute to the progression of the metanephric kidney over time. 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:0003215    cardiac right ventricle morphogenesis    The process in which the right cardiac ventricle is generated and organized.
    GO:0001775    cell activation    A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.
    GO:0001709    cell fate determination    A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.
    GO:0048469    cell maturation    A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state.
    GO:0000902    cell morphogenesis    The developmental process in which the size or shape of a cell is generated and organized.
    GO:0071773    cellular response to BMP stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bone morphogenetic protein (BMP) stimulus.
    GO:0071345    cellular response to cytokine stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
    GO:0035457    cellular response to interferon-alpha    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-alpha stimulus. Interferon-alpha is a type I interferon.
    GO:0071353    cellular response to interleukin-4    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-4 stimulus.
    GO:0071356    cellular response to tumor necrosis factor    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0048589    developmental growth    The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.
    GO:0048565    digestive tract development    The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.
    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:0035162    embryonic hemopoiesis    The stages of blood cell formation that take place within the embryo.
    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:0030218    erythrocyte differentiation    The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
    GO:0048872    homeostasis of number of cells    Any biological process involved in the maintenance of the steady-state number of cells within a population of cells.
    GO:0006959    humoral immune response    An immune response mediated through a body fluid.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0042472    inner ear morphogenesis    The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively.
    GO:0072643    interferon-gamma secretion    The regulated release of interferon-gamma from a cell.
    GO:0072602    interleukin-4 secretion    The regulated release of interleukin-4 from a cell.
    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:0002088    lens development in camera-type eye    The process whose specific outcome is the progression of the lens over time, from its formation to the mature structure. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus.
    GO:0072676    lymphocyte migration    The movement of a lymphocyte within or between different tissues and organs of the body.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0060374    mast cell differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation.
    GO:0060231    mesenchymal to epithelial transition    A transition where a mesenchymal cell establishes apical/basolateral polarity, forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell.
    GO:0001823    mesonephros development    The process whose specific outcome is the progression of the mesonephros over time, from its formation to the mature structure. In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the mesonephros will form the mature kidney.
    GO:1901536    negative regulation of DNA demethylation    Any process that stops, prevents or reduces the frequency, rate or extent of DNA demethylation.
    GO:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:2000146    negative regulation of cell motility    Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:2000607    negative regulation of cell proliferation involved in mesonephros development    Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation involved in mesonephros development.
    GO:2000352    negative regulation of endothelial cell apoptotic process    Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process.
    GO:0045599    negative regulation of fat cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation.
    GO:2000703    negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation    Any process that stops, prevents or reduces the frequency, rate or extent of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation.
    GO:0010629    negative regulation of gene expression    Any process that decreases 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:2000734    negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation    Any process that stops, prevents or reduces the frequency, rate or extent of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0032689    negative regulation of interferon-gamma production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0032703    negative regulation of interleukin-2 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-2 production.
    GO:0033600    negative regulation of mammary gland epithelial cell proliferation    Any process that stops, prevents or reduces the rate or extent of mammary gland epithelial cell proliferation.
    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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0072179    nephric duct formation    The developmental process pertaining to the initial formation of a nephric duct. A nephric duct is a tube that drains a primitive kidney.
    GO:0072178    nephric duct morphogenesis    The process in which the anatomical structures of the nephric duct are generated and organized. A nephric duct is a tube that drains a primitive kidney.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    GO:0001764    neuron migration    The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature.
    GO:0042421    norepinephrine biosynthetic process    The chemical reactions and pathways resulting in the formation of norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine.
    GO:0071599    otic vesicle development    The process whose specific outcome is the progression of the otic vesicle over time, from its formation to the mature structure. The otic vesicle is a transient embryonic structure formed during development of the vertebrate inner ear.
    GO:0060017    parathyroid gland development    The process whose specific outcome is the progression of the parathyroid gland over time, from its formation to the mature structure. The parathyroid gland is an organ specialised for secretion of parathyroid hormone.
    GO:0035898    parathyroid hormone secretion    The regulated release of parathyroid hormone into the circulatory system.
    GO:0060037    pharyngeal system development    The process whose specific outcome is the progression of the pharyngeal system over time, from its formation to the mature structure. The pharyngeal system is a transient embryonic complex that is specific to vertebrates. It comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming: the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear.
    GO:0014065    phosphatidylinositol 3-kinase signaling    A series of reactions within the signal-receiving cell, mediated by the intracellular phosphatidylinositol 3-kinase (PI3K). Many cell surface receptor linked signaling pathways signal through PI3K to regulate numerous cellular functions.
    GO:0045582    positive regulation of T cell differentiation    Any process that activates or increases the frequency, rate or extent of T cell differentiation.
    GO:2000553    positive regulation of T-helper 2 cell cytokine production    Any process that activates or increases the frequency, rate or extent of T-helper 2 cell cytokine production.
    GO:0045597    positive regulation of cell differentiation    Any process that activates or increases the frequency, rate or extent of cell differentiation.
    GO:0001819    positive regulation of cytokine production    Any process that activates or increases the frequency, rate or extent of production of a cytokine.
    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: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:0071442    positive regulation of histone H3-K14 acetylation    Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to histone H3 at position 14 of the histone.
    GO:2000617    positive regulation of histone H3-K9 acetylation    Any process that activates or increases the frequency, rate or extent of histone H3-K9 acetylation.
    GO:0032736    positive regulation of interleukin-13 production    Any process that activates or increases the frequency, rate, or extent of interleukin-13 production.
    GO:2000667    positive regulation of interleukin-13 secretion    Any process that activates or increases the frequency, rate or extent of interleukin-13 secretion.
    GO:0032753    positive regulation of interleukin-4 production    Any process that activates or increases the frequency, rate, or extent of interleukin-4 production.
    GO:0032754    positive regulation of interleukin-5 production    Any process that activates or increases the frequency, rate, or extent of interleukin-5 production.
    GO:2000664    positive regulation of interleukin-5 secretion    Any process that activates or increases the frequency, rate or extent of interleukin-5 secretion.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0009967    positive regulation of signal transduction    Any process that activates or increases the frequency, rate or extent of signal transduction.
    GO:2000611    positive regulation of thyroid hormone generation    Any process that activates or increases the frequency, rate or extent of thyroid hormone generation.
    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:2000679    positive regulation of transcription regulatory region DNA binding    Any process that activates or increases the frequency, rate or extent of transcription regulatory region DNA binding.
    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:0072107    positive regulation of ureteric bud formation    Any process that increases the rate or extent of the developmental process pertaining to the initial formation of the ureteric bud from the Wolffian duct.
    GO:0009791    post-embryonic development    The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
    GO:0002572    pro-T cell differentiation    The process in which a precursor cell type acquires the specialized features of a pro-T cell. Pro-T cells are the earliest stage of the T cell lineage but are not fully committed.
    GO:0043370    regulation of CD4-positive, alpha-beta T cell differentiation    Any process that modulates the frequency, rate, or extent of CD4-positive, alpha-beta T cell differentiation.
    GO:2000683    regulation of cellular response to X-ray    Any process that modulates the frequency, rate or extent of cellular response to X-ray.
    GO:0042035    regulation of cytokine biosynthetic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cytokines.
    GO:2000114    regulation of establishment of cell polarity    Any process that modulates the frequency, rate or extent of establishment of cell polarity.
    GO:0061085    regulation of histone H3-K27 methylation    Any process that modulates the rate, frequency, or extent of histone H3-K27 methylation. Histone H3-K27 methylation is the modification of histone H3 by addition of a methyl group to lysine at position 27 of the histone.
    GO:0051569    regulation of histone H3-K4 methylation    Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
    GO:0072182    regulation of nephron tubule epithelial cell differentiation    Any process that modulates the frequency, rate or extent of nephron tubule epithelial cell differentiation.
    GO:0043523    regulation of neuron apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process in neurons.
    GO:0010975    regulation of neuron projection development    Any process that modulates the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates 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: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:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0043627    response to estrogen    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 stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
    GO:0045471    response to ethanol    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 an ethanol stimulus.
    GO:0010332    response to gamma radiation    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 gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
    GO:0009615    response to virus    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 from a virus.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0048485    sympathetic nervous system development    The process whose specific outcome is the progression of the sympathetic nervous system over time, from its formation to the mature structure. The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter.
    GO:0045061    thymic T cell selection    The process of T cell selection that occurs in the thymus.
    GO:0048538    thymus development    The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components.
    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:0001806    type IV hypersensitivity    An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation.
    GO:0035799    ureter maturation    A developmental process, independent of morphogenetic (shape) change, that is required for the ureter to attain its fully functional state. The ureter is a muscular tube that transports urine from the kidney to the urinary bladder or from the Malpighian tubule to the hindgut.
    GO:0060676    ureteric bud formation    The developmental process pertaining to the initial formation of the ureteric bud from the Wolffian duct. This process begins when the bud protrudes from the duct and ends when it is a recognizable bud.
    GO:0060065    uterus development    The reproductive developmental process whose specific outcome is the progression of the uterus over time, from its formation to the mature structure.
    GO:0003281    ventricular septum development    The progression of the ventricular septum over time from its formation to the mature structure.
cellular component
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3dfx)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3dfx
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GATA3_MOUSE | P23772
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  GATA3_MOUSE | P23772
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GATA3_MOUSE | P237723dfv

(-) Related Entries Specified in the PDB File

3dfv ADJACENT GATA DNA BINDING