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(-) Description

Title :  SOLUTION STRUCTURE OF THE TANDEM HMG BOX DOMAIN FROM HUMAN HIGH MOBILITY GROUP PROTEIN B1
 
Authors :  T. Tomizawa, S. Koshiba, S. Watanabe, T. Harada, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  02 Apr 07  (Deposition) - 12 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Hmg Box Domain, Dna Binding, Helix-Turn-Helix Motif, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Tomizawa, S. Koshiba, S. Watanabe, T. Harada, T. Kigawa, S. Yokoyama
Solution Structure Of The Tandem Hmg Box Domain From Human High Mobility Group Protein B1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HIGH MOBILITY GROUP PROTEIN B1
    ChainsA
    EngineeredYES
    Expression System PlasmidP061030-05
    Expression System Vector TypePLASMID
    FragmentHMG BOX DOMAIN
    GeneHMGB1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymHIGH MOBILITY GROUP PROTEIN 1, HMG-1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2YRQ)

(-) Sites  (0, 0)

(no "Site" information available for 2YRQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

NMR Structure (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_046451G11RHMGB1_HUMANUnclassified  ---AG18R
2UniProtVAR_046452A149EHMGB1_HUMANUnclassified  ---AA156E
3UniProtVAR_046453E156QHMGB1_HUMANPolymorphism  ---AE163Q

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

(-) PROSITE Motifs  (2, 3)

NMR Structure (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.HMGB1_HUMAN9-79
95-163
  2A:16-86
A:102-170
2HMG_BOX_1PS00353 HMG box A DNA-binding domain signature.HMGB1_HUMAN41-52  1A:48-59

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4ENST000003994944ENSE00001538645chr13:31039379-31039210170HMGB1_HUMAN-00--
1.5dENST000003994945dENSE00001384053chr13:31037831-31037668164HMGB1_HUMAN1-50501A:8-5750
1.5gENST000003994945gENSE00000906655chr13:31037489-31037344146HMGB1_HUMAN51-99491A:58-10649
1.6bENST000003994946bENSE00001381337chr13:31036849-31036675175HMGB1_HUMAN99-157591A:106-16459
1.7eENST000003994947eENSE00001538641chr13:31035670-31035044627HMGB1_HUMAN158-215581A:165-1739

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:173
 aligned with HMGB1_HUMAN | P09429 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:173
                                   1                                                                                                                                                                     
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163   
          HMGB1_HUMAN     - -------MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKG 166
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------DUF1898-2yrqA01 A:13-82                                               -------------------HMG_box-2yrqA02 A:102-170                                            --- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------R-----------------------------------------------------------------------------------------------------------------------------------------E------Q---------- SAPs(SNPs)
                PROSITE (1) ---------------HMG_BOX_2  PDB: A:16-86 UniProt: 9-79                                  ---------------HMG_BOX_2  PDB: A:102-170 UniProt: 95-163                            --- PROSITE (1)
                PROSITE (2) -----------------------------------------------HMG_BOX_1   ------------------------------------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) -------Exon 1.5d  PDB: A:8-57 UniProt: 1-50              Exon 1.5g  PDB: A:58-106 UniProt: 51-99          ----------------------------------------------------------Exon 1.7e Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------Exon 1.6b  PDB: A:106-164 UniProt: 99-157                  --------- Transcript 1 (2)
                 2yrq A   1 GSSGSSGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKG 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   

   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  (0, 0)

(no "SCOP Domain" information available for 2YRQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YRQ)

(-) Pfam Domains  (2, 2)

NMR Structure
(-)
Clan: HMG-box (15)

(-) Gene Ontology  (119, 119)

NMR Structure(hide GO term definitions)
Chain A   (HMGB1_HUMAN | P09429)
molecular function
    GO:0019958    C-X-C chemokine binding    Interacting selectively and non-covalently with a C-X-C chemokine; C-X-C chemokines have a single amino acid between the first two cysteines of the characteristic four cysteine motif.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008301    DNA binding, bending    The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
    GO:0070182    DNA polymerase binding    Interacting selectively and non-covalently with a DNA polymerase.
    GO:0050786    RAGE receptor binding    Interacting selectively and non-covalently with the RAGE receptor, the receptor for advanced glycation end-products.
    GO:0000405    bubble DNA binding    Interacting selectively and non-covalently with DNA that contains a bubble. A bubble occurs when DNA contains a region of unpaired, single-stranded DNA flanked on both sides by regions of paired, double-stranded DNA.
    GO:0010858    calcium-dependent protein kinase regulator activity    Modulates the activity of a calcium-dependent protein kinase, an enzyme which phosphorylates a protein in a calcium-dependent manner.
    GO:0042056    chemoattractant activity    Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0000400    four-way junction DNA binding    Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices.
    GO:0001530    lipopolysaccharide binding    Interacting selectively and non-covalently with lipopolysaccharide.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0001786    phosphatidylserine binding    Interacting selectively and non-covalently with phosphatidylserine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of L-serine.
    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:0030295    protein kinase activator activity    Binds to and increases the activity of a protein kinase, an enzyme which phosphorylates a protein.
    GO:0070491    repressing transcription factor binding    Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    GO:0003727    single-stranded RNA binding    Interacting selectively and non-covalently with single-stranded RNA.
    GO:0097100    supercoiled DNA binding    Interacting selectively and non-covalently with supercoiled DNA. For example, during replication and transcription, template DNA is negatively supercoiled in the receding downstream DNA and positively supercoiled in the approaching downstream DNA.
    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.
biological process
    GO:0032392    DNA geometric change    The process in which a transformation is induced in the geometry of a DNA double helix, resulting in a change in twist, writhe, or both, but with no change in linking number. Includes the unwinding of double-stranded DNA by helicases.
    GO:0051103    DNA ligation involved in DNA repair    The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA repair.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006265    DNA topological change    The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
    GO:0035711    T-helper 1 cell activation    The change in morphology and behavior of a T-helper 1 cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0045063    T-helper 1 cell differentiation    The process in which a relatively unspecialized T cell acquires the specialized features of a T-helper 1 (Th1) cell. A Th1 cell is a CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive and produces interferon-gamma.
    GO:0033151    V(D)J recombination    The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).
    GO:0002218    activation of innate immune response    Any process that initiates an innate immune response. Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. Examples of this process include activation of the hypersensitive response of Arabidopsis thaliana and activation of any NOD or TLR signaling pathway in vertebrate species.
    GO:0032147    activation of protein kinase activity    Any process that initiates the activity of an inactive protein kinase.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0006309    apoptotic DNA fragmentation    The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
    GO:0043277    apoptotic cell clearance    The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    GO:0006974    cellular response to DNA damage 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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0031497    chromatin assembly    The assembly of DNA, histone proteins, other associated proteins, and sometimes RNA, into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus.
    GO:0002407    dendritic cell chemotaxis    The movement of a dendritic cell in response to an external stimulus.
    GO:0035767    endothelial cell chemotaxis    The directed movement of an endothelial cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0001935    endothelial cell proliferation    The multiplication or reproduction of endothelial cells, resulting in the expansion of a cell population. Endothelial cells are thin flattened cells which line the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium.
    GO:0001654    eye development    The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight.
    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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0002437    inflammatory response to antigenic stimulus    An inflammatory response to an antigenic stimulus, which can be include any number of T cell or B cell epitopes.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0002281    macrophage activation involved in immune response    A change in morphology and behavior of a macrophage resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response.
    GO:0001773    myeloid dendritic cell activation    The change in morphology and behavior of a dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
    GO:0043371    negative regulation of CD4-positive, alpha-beta T cell differentiation    Any process that stops, prevents, or reduces the frequency, rate, or extent of CD4-positive, alpha-beta T cell differentiation.
    GO:0017055    negative regulation of RNA polymerase II transcriptional preinitiation complex assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
    GO:2000426    negative regulation of apoptotic cell clearance    Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic cell clearance.
    GO:0043537    negative regulation of blood vessel endothelial cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of the migration of the endothelial cells of blood vessels.
    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: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:0031175    neuron projection development    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:0097350    neutrophil clearance    The selective elimination of senescent neutrophils from the body by autoregulatory mechanisms.
    GO:0002270    plasmacytoid dendritic cell activation    A change in the morphology or behavior of a plasmacytoid dendritic cell resulting from exposure to an activating factor such as a cellular or soluble ligand.
    GO:0050918    positive chemotaxis    The directed movement of a motile cell or organism towards a higher concentration of a chemical.
    GO:0043388    positive regulation of DNA binding    Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0051106    positive regulation of DNA ligation    Any process that activates or increases the frequency, rate or extent of DNA ligation, the re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0046330    positive regulation of JNK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:1901224    positive regulation of NIK/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of NIK/NF-kappaB signaling.
    GO:0042104    positive regulation of activated T cell proliferation    Any process that activates or increases the rate or extent of activated T cell proliferation.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0043280    positive regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    GO:0007204    positive regulation of cytosolic calcium ion concentration    Any process that increases the concentration of calcium ions in the cytosol.
    GO:2001200    positive regulation of dendritic cell differentiation    Any process that activates or increases the frequency, rate or extent of dendritic cell differentiation.
    GO:0045819    positive regulation of glycogen catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen.
    GO:0045089    positive regulation of innate immune response    Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
    GO:0032727    positive regulation of interferon-alpha production    Any process that activates or increases the frequency, rate, or extent of interferon-alpha production.
    GO:0032728    positive regulation of interferon-beta production    Any process that activates or increases the frequency, rate, or extent of interferon-beta production.
    GO:0050718    positive regulation of interleukin-1 beta secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 beta from a cell.
    GO:0050716    positive regulation of interleukin-1 secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 from a cell.
    GO:0032733    positive regulation of interleukin-10 production    Any process that activates or increases the frequency, rate, or extent of interleukin-10 production.
    GO:0032735    positive regulation of interleukin-12 production    Any process that activates or increases the frequency, rate, or extent of interleukin-12 production.
    GO:0032755    positive regulation of interleukin-6 production    Any process that activates or increases the frequency, rate, or extent of interleukin-6 production.
    GO:2000778    positive regulation of interleukin-6 secretion    Any process that activates or increases the frequency, rate or extent of interleukin-6 secretion.
    GO:0032425    positive regulation of mismatch repair    Any process that activates or increases the frequency, rate or extent of mismatch repair.
    GO:0090026    positive regulation of monocyte chemotaxis    Any process that increases the frequency, rate, or extent of monocyte chemotaxis.
    GO:0045639    positive regulation of myeloid cell differentiation    Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:1903672    positive regulation of sprouting angiogenesis    Any process that activates or increases the frequency, rate or extent of sprouting angiogenesis.
    GO:0034137    positive regulation of toll-like receptor 2 signaling pathway    Any process that activates or increases the frequency, rate, or extent of toll-like receptor 2 signaling pathway.
    GO:0034145    positive regulation of toll-like receptor 4 signaling pathway    Any process that activates or increases the frequency, rate, or extent of toll-like receptor 4 signaling pathway.
    GO:0034165    positive regulation of toll-like receptor 9 signaling pathway    Any process that activates or increases the frequency, rate, or extent of toll-like receptor 9 signaling pathway.
    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:0032760    positive regulation of tumor necrosis factor production    Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
    GO:0090303    positive regulation of wound healing    Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
    GO:0002840    regulation of T cell mediated immune response to tumor cell    Any process that modulates the frequency, rate, or extent of a T cell mediated immune response to tumor cell.
    GO:0010506    regulation of autophagy    Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:2000819    regulation of nucleotide-excision repair    Any process that modulates the frequency, rate or extent of nucleotide-excision repair.
    GO:0045859    regulation of protein kinase activity    Any process that modulates the frequency, rate or extent of protein kinase activity.
    GO:0032072    regulation of restriction endodeoxyribonuclease activity    Any process that modulates the frequency, rate or extent of a restriction endodeoxyribonuclease activity, the catalysis of endonucleolytic cleavage of DNA in a site-specific manner, resulting in double-strand breaks.
    GO:0002643    regulation of tolerance induction    Any process that modulates the frequency, rate, or extent of tolerance induction.
    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:0051384    response to glucocorticoid    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 glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:1990774    tumor necrosis factor secretion    The regulated release of tumor necrosis factor from a cell. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000793    condensed chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005793    endoplasmic reticulum-Golgi intermediate compartment    A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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:0017053    transcriptional repressor complex    A protein complex that possesses activity that prevents or downregulates transcription.

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