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(-) Description

Title :  SELECTION OF A NOVEL HIGHLY SPECIFIC TNFALPHA ANTAGONIST: INSIGHT FROM THE CRYSTAL STRUCTURE OF THE ANTAGONIST-TNFALPHA COMPLEX
 
Authors :  P. Byla, M. H. Andersen, H. C. Thogersen, H. H. Gad, R. Hartmann
Date :  05 Jan 10  (Deposition) - 23 Feb 10  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  C,T
Keywords :  Tnf-Alpha, Antagonist, In Vitro Selection, Cell Membrane, Cytokine, Disulfide Bond, Glycoprotein, Lipoprotein, Secreted, Signal-Anchor, Transmembrane, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Byla, M. H. Andersen, T. L. Holtet, H. Jacobsen, M. Munch, H. H. Gad, H. C. Thogersen, R. Hartmann
Selection Of A Novel And Highly Specific Tnf{Alpha} Antagonist: Insight From The Crystal Structure Of The Antagonist-Tnf{Alpha} Complex
J. Biol. Chem. V. 285 12096 2010
PubMed-ID: 20179326  |  Reference-DOI: 10.1074/JBC.M109.063305

(-) Compounds

Molecule 1 - TNFALPHA
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT7CIIH6
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - TUMOR NECROSIS FACTOR, SOLUBLE FORM
    ChainsT
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT7CIIH6
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 85-233
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTNF-ALPHA, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 2, TNF-A, CACHECTIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit CT

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH C:202 , HOH C:210 , HOH C:221 , HOH C:245 , HOH C:246 , HOH C:251BINDING SITE FOR RESIDUE MG C 497

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1C:50 -C:60
2C:77 -C:176
3C:152 -C:168
4T:69 -T:101

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L9J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011927A94TTNFA_HUMANPolymorphism1800620TA18T
2UniProtVAR_012318G106STETN_HUMANPolymorphism13963CS85S

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

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.TETN_HUMAN77-198  1C:57-177
2TNF_2PS50049 TNF family profile.TNFA_HUMAN89-233  1T:13-157
3TNF_1PS00251 TNF family signature.TNFA_HUMAN124-140  1T:48-64
4C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.TETN_HUMAN173-197  1C:152-176

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000002961302ENSE00001281126chr3:45067675-45067963289TETN_HUMAN1-37370--
1.4ENST000002961304ENSE00001776827chr3:45072319-4507241799TETN_HUMAN37-70341C:46-494
1.5bENST000002961305bENSE00001927042chr3:45077016-45077563548TETN_HUMAN70-2021331C:49-180 (gaps)132

2.9fENST000003834969fENSE00001901059HSCHR6_MHC_QBL:31533585-31533945361TNFA_HUMAN1-62620--
2.12ENST0000038349612ENSE00001626927HSCHR6_MHC_QBL:31534554-3153459946TNFA_HUMAN63-78160--
2.13ENST0000038349613ENSE00001681816HSCHR6_MHC_QBL:31534787-3153483448TNFA_HUMAN78-94171T:9-1810
2.14bENST0000038349614bENSE00001902809HSCHR6_MHC_QBL:31535136-315363561221TNFA_HUMAN94-2331401T:18-157140

(-) 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 C from PDB  Type:PROTEIN  Length:130
 aligned with TETN_HUMAN | P05452 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:135
                                    76        86        96       106       116       126       136       146       156       166       176       186       196     
           TETN_HUMAN    67 LQTVCLKGTKVHMKCFLAFTQTKTFHEASEDCISRGGTLGTPQTGSENDALYEYLRQSVGNEAEIWLGLNDMAAEGTWVDMTGARIAYKNWETEITAQPDGGKTENCAVLSGAANGKWFDKRCRDQLPYICQFGI 201
               SCOP domains d3l9jc     _ C: automated matches                                                                                                       SCOP domains
               CATH domains 3l9jC0     0 C:46-180 Mannose-Binding Protein A, subunit A                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee-----.eeeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhh....eee..ee........ee............hhhhhh........eeeee......eeee.....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------S----------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------C_TYPE_LECTIN_2  PDB: C:57-177 UniProt: 77-198                                                                            --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1          ---- PROSITE (3)
           Transcript 1 (1) 1.4 ----------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.5b  PDB: C:49-180 (gaps) UniProt: 70-202 [INCOMPLETE]                                                                         Transcript 1 (2)
                 3l9j C  46 LQTVCL-----HMKCFLAFTQTKTFHEASEDCISRGGTLSTPQTGSENDALYEYLRQSVGNEAEIWLGLNKRWSRYFWVDMTGTRIAYKNWEHSSDAQPDPSNWENCAVLSGAANGKWFGKRCRDQLPYICQFGI 180
                                 |   - |      65        75        85        95       105       115       125       135       145       155       165       175     
                                51    57                                                                                                                           

Chain T from PDB  Type:PROTEIN  Length:149
 aligned with TNFA_HUMAN | P01375 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:149
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224         
           TNFA_HUMAN    85 SDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL 233
               SCOP domains d3l9jt_ T: Tumor necrosis factor (TNF)                                                                                                                SCOP domains
               CATH domains 3l9jT00 T:9-157  [code=2.60.120.40, no name defined]                                                                                                  CATH domains
               Pfam domains -----------------TNF-3l9jT01 T:26-157                                                                                                                 Pfam domains
         Sec.struct. author ....eeeeee.........ee......eee...eee..eee....eeeeeeeeeeeeee........eeeeeeee......eeeeeeeee..............eeeeeeeeeeeeee....eeeeee.hhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------T------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----TNF_2  PDB: T:13-157 UniProt: 89-233                                                                                                              PROSITE (2)
                PROSITE (3) ---------------------------------------TNF_1            --------------------------------------------------------------------------------------------- PROSITE (3)
           Transcript 2 (1) Exon 2.13 ------------------------------------------------------------------------------------------------------------------------------------------- Transcript 2 (1)
           Transcript 2 (2) ---------Exon 2.14b  PDB: T:18-157 UniProt: 94-233                                                                                                    Transcript 2 (2)
                 3l9j T   9 SDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL 157
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148         

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: C1q_TNF (45)

(-) Gene Ontology  (162, 164)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C   (TETN_HUMAN | P05452)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0036143    kringle domain binding    Interacting selectively and non-covalently with a kringle domain. Kringle domains are protein domains that fold into large loops stabilized by 3 disulfide linkages, and are important in protein-protein interactions with blood coagulation factors.
biological process
    GO:0030282    bone mineralization    The deposition of hydroxyapatite, a form of calcium phosphate with the formula Ca10(PO4)6(OH)2, in bone tissue.
    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:0071560    cellular response to transforming growth factor beta 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 transforming growth factor beta stimulus.
    GO:0001503    ossification    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0010756    positive regulation of plasminogen activation    Any process that increases the rate, frequency or extent of plasminogen activation. Plasminogen activation is the process in which plasminogen is processed to plasmin.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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:0001652    granular component    A structure found in the nucleolus, which contains nearly completed preribosomal particles destined for the cytoplasm.
    GO:0031089    platelet dense granule lumen    The volume enclosed by the membrane of the platelet dense granule.

Chain T   (TNFA_HUMAN | P01375)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    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: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:0005164    tumor necrosis factor receptor binding    Interacting selectively and non-covalently with the tumor necrosis factor receptor.
biological process
    GO:0007249    I-kappaB kinase/NF-kappaB signaling    The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
    GO:0007254    JNK cascade    An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (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: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:0000185    activation of MAPKKK activity    Any process that initiates the activity of the inactive enzyme MAP kinase kinase kinase (MAPKKK).
    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:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0097190    apoptotic signaling pathway    A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
    GO:0045123    cellular extravasation    The migration of a leukocyte from the blood vessels into the surrounding tissue.
    GO:0071230    cellular response to amino acid 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 an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    GO:0071222    cellular response to lipopolysaccharide    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 lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0071316    cellular response to nicotine    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 nicotine 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:0002439    chronic inflammatory response to antigenic stimulus    A chronic inflammatory response to an antigenic stimulus. A chronic inflammatory response persists indefinitely during days, weeks, or months in the life of an individual.
    GO:0030866    cortical actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of actin-based cytoskeletal structures in the cell cortex, i.e. just beneath the plasma membrane.
    GO:0071550    death-inducing signaling complex assembly    A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by a death domain (DD) interaction, as part of the extrinsic apoptotic signaling pathway.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0048566    embryonic digestive tract development    The process whose specific outcome is the progression of the gut over time, from its formation to the mature structure during embryonic development. The gut is the region of the digestive tract extending from the beginning of the intestines to the anus.
    GO:0060664    epithelial cell proliferation involved in salivary gland morphogenesis    The multiplication or reproduction of epithelial cells of the submandibular salivary gland, resulting in the expansion of a cell population and the shaping of the gland.
    GO:0090002    establishment of protein localization to plasma membrane    The directed movement of a protein to a specific location in the plasma membrane.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    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:0008625    extrinsic apoptotic signaling pathway via death domain receptors    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 a ligand binding to a death domain receptor on the cell surface, and ends when the execution phase of apoptosis is triggered.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    GO:0006959    humoral immune response    An immune response mediated through a body fluid.
    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:0008630    intrinsic apoptotic signaling pathway in response to DNA damage    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0050901    leukocyte tethering or rolling    Transient adhesive interactions between leukocytes and endothelial cells lining blood vessels. Carbohydrates on circulating leukocytes bind selectins on the vessel wall causing the leukocytes to slow down and roll along the inner surface of the vessel wall. During this rolling motion, transitory bonds are formed and broken between selectins and their ligands. Typically the first step in cellular extravasation (the movement of leukocytes out of the circulatory system, towards the site of tissue damage or infection).
    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:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0097527    necroptotic signaling pathway    A series of molecular signals which triggers the necroptotic death of a cell. The pathway starts with reception of a signal, is characterized by activation of receptor-interacting serine/threonine-protein kinase 1 and/or 3 (RIPK1/3, also called RIP1/3), and ends when the execution phase of necroptosis is triggered.
    GO:0010693    negative regulation of alkaline phosphatase activity    Any process that decreases 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:1903347    negative regulation of bicellular tight junction assembly    Any process that stops, prevents or reduces the frequency, rate or extent of tight junction assembly.
    GO:0061048    negative regulation of branching involved in lung morphogenesis    Any process that decreases the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.
    GO:0002740    negative regulation of cytokine secretion involved in immune response    Any process that stops, prevents, or reduces the frequency, rate, or extent of cytokine secretion contributing to an immune response.
    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:0045599    negative regulation of fat cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0046325    negative regulation of glucose import    Any process that stops, prevents, or reduces the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle.
    GO:0044130    negative regulation of growth of symbiont in host    Any process in which the symbiont stops, prevents or reduces its increase in size or mass within the cells or tissues of the host organism. The host is defined as the larger of the organisms involved in the symbiotic interaction.
    GO:0032715    negative regulation of interleukin-6 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production.
    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:0010888    negative regulation of lipid storage    Any process that decreases the rate, frequency or extent of lipid storage. Lipid storage is the accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development.
    GO:0045662    negative regulation of myoblast differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
    GO:0035509    negative regulation of myosin-light-chain-phosphatase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of myosin-light-chain-phosphatase activity.
    GO:0045668    negative regulation of osteoblast differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation.
    GO:0043242    negative regulation of protein complex disassembly    Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045071    negative regulation of viral genome replication    Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
    GO:0006927    obsolete transformed cell apoptotic process    OBSOLETE. Any apoptotic process in a transformed cell, a cell that has undergone changes manifested by escape from control mechanisms, increased growth potential, alterations in the cell surface, karyotypic abnormalities, morphological and biochemical deviations from the norm.
    GO:0030316    osteoclast differentiation    The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue.
    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: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:0043507    positive regulation of JUN kinase activity    Any process that activates or increases the frequency, rate or extent of JUN kinase activity.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    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:0051533    positive regulation of NFAT protein import into nucleus    Any process that activates or increases the frequency, rate or extent of the movement of an NFAT protein from the cytoplasm to the nucleus.
    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:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:2000334    positive regulation of blood microparticle formation    Any process that activates or increases the frequency, rate or extent of blood microparticle formation.
    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:0045785    positive regulation of cell adhesion    Any process that activates or increases the frequency, rate or extent of cell adhesion.
    GO:2000304    positive regulation of ceramide biosynthetic process    Any process that activates or increases the frequency, rate or extent of ceramide biosynthetic process.
    GO:2000343    positive regulation of chemokine (C-X-C motif) ligand 2 production    Any process that activates or increases the frequency, rate or extent of chemokine (C-X-C motif) ligand 2 production.
    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:0032722    positive regulation of chemokine production    Any process that activates or increases the frequency, rate, or extent of chemokine production.
    GO:0002876    positive regulation of chronic inflammatory response to antigenic stimulus    Any process that activates or increases the frequency, rate, or extent of a chronic inflammatory response to an antigenic stimulus.
    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:0001819    positive regulation of cytokine production    Any process that activates or increases the frequency, rate or extent of production of a cytokine.
    GO:0050715    positive regulation of cytokine secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of cytokines from a cell.
    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:0051798    positive regulation of hair follicle development    Any process that activates or increases the frequency, rate or extent of hair follicle development.
    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:0002925    positive regulation of humoral immune response mediated by circulating immunoglobulin    Any process that activates or increases the frequency, rate, or extent of a humoral immune response mediated by circulating immunoglobulin.
    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:0032755    positive regulation of interleukin-6 production    Any process that activates or increases the frequency, rate, or extent of interleukin-6 production.
    GO:0045416    positive regulation of interleukin-8 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-8.
    GO:0032757    positive regulation of interleukin-8 production    Any process that activates or increases the frequency, rate, or extent of interleukin-8 production.
    GO:1904999    positive regulation of leukocyte adhesion to arterial endothelial cell    Any process that activates or increases the frequency, rate or extent of leukocyte adhesion to arterial endothelial cell.
    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:0071677    positive regulation of mononuclear cell migration    Any process that increases the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body.
    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:0045672    positive regulation of osteoclast differentiation    Any process that activates or increases the frequency, rate or extent of osteoclast differentiation.
    GO:0033138    positive regulation of peptidyl-serine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:0071803    positive regulation of podosome assembly    Any process that activates or increases the rate or extent of podosome assembly.
    GO:0043068    positive regulation of programmed cell death    Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
    GO:0031334    positive regulation of protein complex assembly    Any process that activates or increases the frequency, rate or extent of protein complex assembly.
    GO:0043243    positive regulation of protein complex disassembly    Any process that activates or increases the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0045860    positive regulation of protein kinase activity    Any process that activates or increases the frequency, rate or extent of protein kinase activity.
    GO:2000010    positive regulation of protein localization to cell surface    Any process that activates or increases the frequency, rate or extent of protein localization to the cell surface.
    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:0051222    positive regulation of protein transport    Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0048661    positive regulation of smooth muscle cell proliferation    Any process that activates or increases the rate or extent of smooth muscle cell proliferation.
    GO:1901671    positive regulation of superoxide dismutase activity    Any process that activates or increases the frequency, rate or extent of superoxide dismutase activity.
    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:0045994    positive regulation of translational initiation by iron    Any process involving iron that activates or increases the rate of translational initiation.
    GO:0060557    positive regulation of vitamin D biosynthetic process    Any process that increases the rate, frequency or extent of a vitamin D biosynthetic process. Vitamin D biosynthesis is the chemical reactions and pathways resulting in the formation of vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3).
    GO:0000060    protein import into nucleus, translocation    A protein transport process that contributes to protein import into the nucleus, and that results in the vectorial transfer of a cargo-carrier protein complex through the nuclear pore complex from the cytoplasmic side to the nucleoplasmic side of the nuclear envelope.
    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:0032800    receptor biosynthetic process    The chemical reactions and pathways resulting in the formation of a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0043122    regulation of I-kappaB kinase/NF-kappaB signaling    Any process that modulates I-kappaB kinase/NF-kappaB signaling.
    GO:0060693    regulation of branching involved in salivary gland morphogenesis    Any process that modulates the rate, frequency, or extent of branching morphogenesis in the salivary gland epithelium.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:1903140    regulation of establishment of endothelial barrier    Any process that modulates the frequency, rate or extent of establishment of endothelial barrier.
    GO:0051023    regulation of immunoglobulin secretion    Any process that modulates the frequency, rate or extent of the regulated release of immunoglobulins from a cell.
    GO:0050796    regulation of insulin secretion    Any process that modulates the frequency, rate or extent of the regulated release of insulin.
    GO:0045670    regulation of osteoclast differentiation    Any process that modulates the frequency, rate or extent of osteoclast differentiation.
    GO:0001932    regulation of protein phosphorylation    Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein.
    GO:0050708    regulation of protein secretion    Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell.
    GO:2000377    regulation of reactive oxygen species metabolic process    Any process that modulates the frequency, rate or extent of reactive oxygen species metabolic process.
    GO:0010803    regulation of tumor necrosis factor-mediated signaling pathway    Any process that modulates the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor.
    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:0010033    response to organic substance    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 organic substance stimulus.
    GO:0009651    response to salt stress    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 an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
    GO:0009615    response to virus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
    GO: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.
    GO:0033209    tumor necrosis factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0001891    phagocytic cup    An invagination of the cell membrane formed by an actin dependent process during phagocytosis. Following internalization it is converted into a phagosome.
    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:0055037    recycling endosome    An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TETN_HUMAN | P054521htn 1rjh 1tn3
        TNFA_HUMAN | P013751a8m 1tnf 2az5 2e7a 2tun 2zjc 2zpx 3alq 3it8 3wd5 4g3y 4tsv 4twt 4y6o 5mu8 5tsw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3L9J)