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(-) Description

Title :  CRYSTAL STRUCTURE OF CHICKEN IL-1 HYDROPHOBIC CAVITY MUTANT 157
 
Authors :  H. S. Yin, Y. W. Chen
Date :  17 Jun 10  (Deposition) - 22 Jun 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym./Biol. Unit :  A
Keywords :  Chicken, Interleukin-1 Beta, Hydrophobic Cavity Mutant, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. S. Cheng, W. T. Chen, L. H. Lee, Y. W. Chen, S. Y. Chang, P. C. Lyu, H. S. Yin
Structural And Functional Comparison Of Cytokine Interleukin-1 Beta From Chicken And Human
Mol. Immunol. V. 48 947 2011
PubMed-ID: 21288573  |  Reference-DOI: 10.1016/J.MOLIMM.2011.01.002

(-) Compounds

Molecule 1 - IL-1 BETA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
    SynonymINTERLEUKIN-1 BETA, INTERLEUKIN-1BETA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3NJ5)

(-) Sites  (0, 0)

(no "Site" information available for 3NJ5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NJ5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NJ5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NJ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NJ5)

(-) Exons   (0, 0)

(no "Exon" information available for 3NJ5)

(-) 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:152
 aligned with O73909_CHICK | O73909 from UniProtKB/TrEMBL  Length:267

    Alignment length:159
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257         
         O73909_CHICK   108 AFRYTRSQSFDIFDINQKCFVLESPTQLVALHLQGPSSSQKVRLNIALYRPRGPRGSAGTGQMPVALGIKGYKLYMSCVMSGTEPTLQLEEADVMRDIDSVELTRFIFYRLDSPTEGTTRFESAAFPGWFICTSLQPRQPVGITNQPDQVNIATYKLSG 266
               SCOP domains d3nj5a_ A: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------IL1-3nj5A01 A:35-158                                                                                                        --- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee....eeeeee..eeeee............eeeeeee....-------..eeeeee....eeeeeeee..eeeeeeee.....ee...hhhhh.eeeeee....eeeeee......eee......ee.eee..........eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nj5 A   3 AFRYTRSQSFDIFDINQKCFVLESPTQLVALHLQGPSSSQKVRLNIALYRPRGP-------QMPVALGIKGYKLYMSCVMSGTEPTLQLEEADVMRDIDSVELTRFIFYRLDSPTEGTTRFESAAFPGWFICTSLQPRQPVGITNQPDQVNIATFKLSG 161
                                    12        22        32        42        52   |     - |      72        82        92       102       112       122       132       142       152         
                                                                                56      64                                                                                                 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NJ5)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Trefoil (131)

(-) Gene Ontology  (77, 77)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O73909_CHICK | O73909)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0005149    interleukin-1 receptor binding    Interacting selectively and non-covalently with the interleukin-1 receptor.
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
biological process
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    GO:0006953    acute-phase response    An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
    GO:0035690    cellular response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0071260    cellular response to mechanical 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 mechanical stimulus.
    GO:0071407    cellular response to organic cyclic compound    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0071310    cellular response to organic substance    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
    GO:0032602    chemokine production    The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0043400    cortisol secretion    The regulated release of cortisol, a steroid hormone that in humans is the major circulating hormone of the cortex, or outer layer, of the adrenal gland.
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0035234    ectopic germ cell programmed cell death    Programmed cell death of an errant germ line cell that is outside the normal migratory path or ectopic to the gonad. This is an important mechanism of regulating germ cell survival within the embryo.
    GO:0097192    extrinsic apoptotic signaling pathway in absence of ligand    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 withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered.
    GO:0001660    fever generation    The heat generation process that results in a rise in body temperature above the normal, often as a response to infection.
    GO:0030213    hyaluronan biosynthetic process    The chemical reactions and pathways resulting in the formation of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
    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: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:0032611    interleukin-1 beta production    The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0031663    lipopolysaccharide-mediated signaling pathway    A series of molecular signals initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system.
    GO:0070487    monocyte aggregation    The adhesion of one monocyte to one or more other monocytes via adhesion molecules.
    GO:0043407    negative regulation of MAP kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity.
    GO:0070164    negative regulation of adiponectin secretion    Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of adiponectin from a cell.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:2001240    negative regulation of extrinsic apoptotic signaling pathway in absence of ligand    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.
    GO:0010829    negative regulation of glucose transport    Any process that decreases the frequency, rate or extent of glucose transport. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0046627    negative regulation of insulin receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling.
    GO:0050995    negative regulation of lipid catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids.
    GO:0045833    negative regulation of lipid metabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    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:0042346    positive regulation of NF-kappaB import into nucleus    Any process that activates or increases the frequency, rate or extent of transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0060559    positive regulation of calcidiol 1-monooxygenase activity    Any process that increases the rate, frequency or extent of calcidiol 1-monooxygenase activity. Calcidiol 1-monooxygenase activity is the catalysis of the reaction: calcidiol + NADPH + H+ + O2 = calcitriol + NADP+ + H2O.
    GO:0051781    positive regulation of cell division    Any process that activates or increases the frequency, rate or extent of cell division.
    GO:0045080    positive regulation of chemokine biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of chemokines.
    GO:0031622    positive regulation of fever generation    Any process that activates or increases the frequency, rate, or extent of fever generation.
    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:0032725    positive regulation of granulocyte macrophage colony-stimulating factor production    Any process that activates or increases the frequency, rate, or extent of granulocyte macrophage colony-stimulating factor production.
    GO:0034116    positive regulation of heterotypic cell-cell adhesion    Any process that activates or increases the frequency, rate, or extent of heterotypic cell-cell adhesion.
    GO:0032729    positive regulation of interferon-gamma production    Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0045086    positive regulation of interleukin-2 biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-2.
    GO:0045410    positive regulation of interleukin-6 biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-6.
    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:0032757    positive regulation of interleukin-8 production    Any process that activates or increases the frequency, rate, or extent of interleukin-8 production.
    GO:0050996    positive regulation of lipid catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids.
    GO:0051044    positive regulation of membrane protein ectodomain proteolysis    Any process that activates or increases the frequency, rate or extent of membrane protein ectodomain peptidolysis.
    GO:0045840    positive regulation of mitotic nuclear division    Any process that activates or increases the frequency, rate or extent of mitosis.
    GO:0071639    positive regulation of monocyte chemotactic protein-1 production    Any process that activates or increases the frequency, rate, or extent of production of monocyte chemotactic protein-1.
    GO:0035505    positive regulation of myosin light chain kinase activity    Any process that activates or increases the frequency, rate or extent of myosin light chain kinase activity.
    GO:0045429    positive regulation of nitric oxide biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:0032308    positive regulation of prostaglandin secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of a prostaglandin from a cell.
    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:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    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:0010575    positive regulation of vascular endothelial growth factor production    Any process that increases or activates the frequency, rate, or extent of production of vascular endothelial growth factor.
    GO:0043491    protein kinase B signaling    A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase B (also called AKT), which occurs as a result of a single trigger reaction or compound.
    GO:0043122    regulation of I-kappaB kinase/NF-kappaB signaling    Any process that modulates I-kappaB kinase/NF-kappaB signaling.
    GO:1903140    regulation of establishment of endothelial barrier    Any process that modulates the frequency, rate or extent of establishment of endothelial barrier.
    GO:0050796    regulation of insulin secretion    Any process that modulates the frequency, rate or extent of the regulated release of insulin.
    GO:0050999    regulation of nitric-oxide synthase activity    Any process that modulates the activity of the enzyme nitric-oxide synthase.
    GO:0033198    response to ATP    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ATP (adenosine 5'-triphosphate) stimulus.
    GO:0009743    response to carbohydrate    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 carbohydrate stimulus.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0030730    sequestering of triglyceride    The process of binding or confining any triester of glycerol such that it is separated from other components of a biological system.
cellular component
    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:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
    GO:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

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        O73909_CHICK | O739092wry 4x37 4x38 4x39 4x3a

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