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(-) Description

Title :  CRYSTAL STRUCTURE OF SMAD3-MH1 BOUND TO DNA AT 2.4 A RESOLUTION
 
Authors :  J. Chai, J. -W. Wu, N. Yan, J. Massague, N. P. Pavletich, Y. Shi
Date :  09 Apr 03  (Deposition) - 23 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Smad, Mad Homology Domain 1, Dna Recognition, Tgf-Beta Signaling, Zinc-Binding Module, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Chai, J. -W. Wu, N. Yan, J. Massague, N. P. Pavletich, Y. Shi
Features Of A Smad3 Mh1-Dna Complex. Roles Of Water And Zinc In Dna Binding.
J. Biol. Chem. V. 278 20327 2003
PubMed-ID: 12686552  |  Reference-DOI: 10.1074/JBC.C300134200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SMAD BINDING ELEMENT
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 2 - SMAD BINDING ELEMENT
    ChainsD
    EngineeredYES
    SyntheticYES
 
Molecule 3 - SMAD 3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentDWA DOMAIN
    GeneMADH3 OR SMAD3 OR MAD3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMOTHERS AGAINST DPP HOMOLOG 3, MAD3, HMAD-3, MMAD3, JV15-2, HSMAD3

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

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:64 , CYS A:109 , CYS A:121 , HIS A:126BINDING SITE FOR RESIDUE ZN A 145
2AC2SOFTWARECYS B:64 , CYS B:109 , CYS B:121 , HIS B:126BINDING SITE FOR RESIDUE ZN B 145

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_067051A112VSMAD3_HUMANDisease (LDS3)387906854A/BA112V

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MH1PS51075 MAD homology domain 1 (MH1) profile.SMAD3_HUMAN10-136
 
  2A:10-132
B:10-132

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003273671ENSE00001346645chr15:67358183-67358698516SMAD3_HUMAN1-69692A:7-69
B:9-69
63
61
1.3ENST000003273673ENSE00001108083chr15:67457233-67457426194SMAD3_HUMAN69-134662A:69-132
B:69-132
64
64
1.4ENST000003273674ENSE00001299299chr15:67457591-67457722132SMAD3_HUMAN134-178450--
1.5ENST000003273675ENSE00001639631chr15:67459117-6745919175SMAD3_HUMAN178-203260--
1.6ENST000003273676ENSE00001108077chr15:67462892-6746294251SMAD3_HUMAN203-220180--
1.7ENST000003273677ENSE00001108067chr15:67473579-67473791213SMAD3_HUMAN220-291720--
1.8ENST000003273678ENSE00001108070chr15:67477065-67477202138SMAD3_HUMAN291-337470--
1.9ENST000003273679ENSE00001684341chr15:67479703-67479847145SMAD3_HUMAN337-385490--
1.10bENST0000032736710bENSE00001346632chr15:67482751-674875334783SMAD3_HUMAN385-425410--

(-) 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:126
 aligned with SMAD3_HUMAN | P84022 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:126
                                    16        26        36        46        56        66        76        86        96       106       116       126      
         SMAD3_HUMAN      7 FTPPIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNVNTKCITIPRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNPYHYQRVET  132
               SCOP domains d1ozja_ A: SMAD MH1 domain                                                                                                     SCOP domains
               CATH domains 1ozjA00 A:7-132 Smad3; Chain A                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......eee......eee..eeehhhhhhhhhhh.....hhh.eee......hhhhh..eee.hhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------V-------------------- SAPs(SNPs)
                    PROSITE ---MH1  PDB: A:10-132 UniProt: 10-136                                                                                          PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:7-69 UniProt: 1-69 [INCOMPLETE]               --------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------Exon 1.3  PDB: A:69-132 UniProt: 69-134 [INCOMPLETE]             Transcript 1 (2)
                1ozj A    7 FTPPIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNVNTKCITIPRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNPYHYQRVET  132
                                    16        26        36        46        56        66        76        86        96       106       116       126      

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with SMAD3_HUMAN | P84022 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:124
                                    18        28        38        48        58        68        78        88        98       108       118       128    
         SMAD3_HUMAN      9 PPIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNVNTKCITIPRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNPYHYQRVET  132
               SCOP domains d1ozjb_ B: SMAD MH1 domain                                                                                                   SCOP domains
               CATH domains 1ozjB00 B:9-132 Smad3; Chain A                                                                                               CATH domains
           Pfam domains (1) ----------------------MH1-1ozjB01 B:31-131                                                                                 - Pfam domains (1)
           Pfam domains (2) ----------------------MH1-1ozjB02 B:31-131                                                                                 - Pfam domains (2)
         Sec.struct. author hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......eee......eee..eeehhhhhhhhhhh.....hhh.eee......hhhhh..eee.hhh.eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------V-------------------- SAPs(SNPs)
                    PROSITE -MH1  PDB: B:10-132 UniProt: 10-136                                                                                          PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:9-69 UniProt: 1-69 [INCOMPLETE]             --------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------Exon 1.3  PDB: B:69-132 UniProt: 69-134 [INCOMPLETE]             Transcript 1 (2)
                1ozj B    9 PPIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNVNTKCITIPRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNPYHYQRVET  132
                                    18        28        38        48        58        68        78        88        98       108       118       128    

Chain C from PDB  Type:DNA  Length:15
                                                
                1ozj C 1001 TCAGTCTAGACATAC 1015
                                  1010     

Chain D from PDB  Type:DNA  Length:15
                                                
                1ozj D 2001 GTATGTCTAGACTGA 2015
                                  2010     

   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  (1, 2)

Asymmetric/Biological Unit
(-)
Family: MH1 (4)
1aMH1-1ozjB01B:31-131
1bMH1-1ozjB02B:31-131

(-) Gene Ontology  (120, 120)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SMAD3_HUMAN | P84022)
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.

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        SMAD3_HUMAN | P840221mhd 1mjs 1mk2 1u7f 2laj 2lb2

(-) Related Entries Specified in the PDB File

1mhd