1MHD | PD0243 - JenaLib

Asymmetric/Biological Unit(hide GO term definitions)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0070412	R-SMAD binding	Interacting selectively and non-covalently with a receptor-regulated SMAD signaling protein.
	GO:0001102	RNA polymerase II activating transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
	GO:0000978	RNA polymerase II 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 a core promoter for RNA polymerase II.
	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:0046332	SMAD binding	Interacting selectively and non-covalently with a SMAD signaling protein.
	GO:0043425	bHLH transcription factor binding	Interacting selectively and non-covalently with any of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors, important regulatory components in transcriptional networks of many developmental pathways.
	GO:0031490	chromatin DNA binding	Interacting selectively and non-covalently with DNA that is assembled into chromatin.
	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:0070410	co-SMAD binding	Interacting selectively and non-covalently with a common mediator SMAD signaling protein.
	GO:0005518	collagen binding	Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
	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:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0035326	enhancer binding	Interacting selectively and non-covalently with an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019902	phosphatase binding	Interacting selectively and non-covalently with any phosphatase.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	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:0000983	transcription factor activity, RNA polymerase II core promoter sequence-specific	Interacting selectively and non-covalently with a specific DNA sequence in an RNA polymerase II (Pol II) core promoter, the region composed of the transcription start site and binding sites for transcription factors of the Pol II basal transcription machinery, in order to modulate transcription by Pol II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0000988	transcription factor activity, 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), in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
	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:0005160	transforming growth factor beta receptor binding	Interacting selectively and non-covalently with the transforming growth factor beta receptor.
	GO:0030618	transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity	A TGF-beta cytoplasmic mediator that is phosphorylated by a TGFbeta receptor and complexes with a common-partner mediator. The- heterocomplex translocates to the nucleus to regulate transcription.
	GO:0043130	ubiquitin binding	Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0007183	SMAD protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex that contains SMAD proteins.
	GO:0060395	SMAD protein signal transduction	The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell.
	GO:0042110	T cell activation	The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0006919	activation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
	GO:0097296	activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway	Any process that initiates the activity of an inactive cysteine-type endopeptidase involved in the apoptotic signaling pathway.
	GO:0032924	activin receptor signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to an activin receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0007050	cell cycle arrest	A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
	GO:0045216	cell-cell junction organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-cell junction. A cell-cell junction is a specialized region of connection between two cells.
	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: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:0048617	embryonic foregut morphogenesis	The process in which the anatomical structures of the foregut are generated and organized, during the embryonic phase.
	GO:0009880	embryonic pattern specification	The process that results in the patterns of cell differentiation that will arise in an embryo.
	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:0019049	evasion or tolerance of host defenses by virus	Any process, either active or passive, by which a virus avoids or tolerates the effects of its host organism's defense(s). Host defenses may be induced by the presence of the virus or may be preformed (e.g. physical barriers). The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0097191	extrinsic apoptotic signaling pathway	A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered.
	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: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:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002520	immune system development	The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process.
	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:0070306	lens fiber cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a lens fiber cell, any of the elongated, tightly packed cells that make up the bulk of the mature lens in the camera-type eye. The cytoplasm of a lens fiber cell is devoid of most intracellular organelles including the cell nucleus, and contains primarily crystallins, a group of water-soluble proteins expressed in vary large quantities.
	GO:0001889	liver development	The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
	GO:0001707	mesoderm formation	The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0030308	negative regulation of cell growth	Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0045599	negative regulation of fat cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation.
	GO:0050728	negative regulation of inflammatory response	Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
	GO:0045930	negative regulation of mitotic cell cycle	Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle.
	GO:0045668	negative regulation of osteoblast differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation.
	GO:0033689	negative regulation of osteoblast proliferation	Any process that stops, prevents or reduces the rate or extent of osteoblast 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:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway.
	GO:0061045	negative regulation of wound healing	Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
	GO:0038092	nodal signaling pathway	A series of molecular signals initiated by the binding of a nodal protein to an activin receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0002076	osteoblast development	The process whose specific outcome is the progression of an osteoblast over time, from its formation to the mature structure. Osteoblast development does not include the steps involved in committing a cranial neural crest cell or an osteoprogenitor cell to an osteoblast fate. An osteoblast is a cell that gives rise to bone.
	GO:0001649	osteoblast differentiation	The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
	GO:0048340	paraxial mesoderm morphogenesis	The process in which the anatomical structures of the paraxial mesoderm are generated and organized.
	GO:0060039	pericardium development	The process whose specific outcome is the progression of the pericardium over time, from its formation to the mature structure. The pericardium is a double-walled sac that contains the heart and the roots of the aorta, vena cava and the pulmonary artery.
	GO:0010694	positive regulation of alkaline phosphatase activity	Any process that increases the frequency, rate or extent of alkaline phosphatase activity, the catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.
	GO:0030501	positive regulation of bone mineralization	Any process that activates or increases the frequency, rate or extent of bone mineralization.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0032332	positive regulation of chondrocyte differentiation	Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation.
	GO:0010718	positive regulation of epithelial to mesenchymal transition	Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
	GO:1901203	positive regulation of extracellular matrix assembly	Any process that activates or increases the frequency, rate or extent of extracellular matrix assembly.
	GO:0051894	positive regulation of focal adhesion assembly	Any process that activates or increases the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
	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:0032731	positive regulation of interleukin-1 beta production	Any process that activates or increases the frequency, rate, or extent of interleukin-1 beta production.
	GO:0050927	positive regulation of positive chemotaxis	Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
	GO:0051496	positive regulation of stress fiber assembly	Any process that activates or increases the frequency, rate or extent of the assembly of a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.
	GO:0042993	positive regulation of transcription factor import into nucleus	Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus.
	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:0032916	positive regulation of transforming growth factor beta3 production	Any process that activates or increases the frequency, rate, or extent of production of transforming growth factor-beta3.
	GO:0031053	primary miRNA processing	Any process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule.
	GO:0051098	regulation of binding	Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
	GO:0050678	regulation of epithelial cell proliferation	Any process that modulates the frequency, rate or extent of epithelial cell proliferation.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
	GO:0016202	regulation of striated muscle tissue development	Any process that modulates the frequency, rate or extent of striated muscle development.
	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:0017015	regulation of transforming growth factor beta receptor signaling pathway	Any process that modulates the frequency, rate or extent of activity of any TGF-beta receptor signaling pathway.
	GO:0032909	regulation of transforming growth factor beta2 production	Any process that modulates the frequency, rate, or extent of production of transforming growth factor-beta2.
	GO:0001666	response to hypoxia	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	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: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:0030878	thyroid gland development	The process whose specific outcome is the progression of the thyroid gland over time, from its formation to the mature structure. The thyroid gland is an endoderm-derived gland that produces thyroid hormone.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0060290	transdifferentiation	The conversion of a differentiated cell of one fate into a differentiated cell of another fate without first undergoing cell division or reversion to a more primitive or stem cell-like fate.
	GO:0007179	transforming growth factor beta receptor signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	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:0042060	wound healing	The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
	GO:0071141	SMAD protein complex	A protein complex that consists of only SMAD proteins; may be homomeric or heteromeric.
	GO:0071144	SMAD2-SMAD3 protein complex	A heteromeric SMAD protein complex that contains SMAD2 and SMAD3.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	GO:0005637	nuclear inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0043235	receptor complex	Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	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.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (1, 2)

Exons (2, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (120, 120)

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Related Entries Specified in the PDB File