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(-) Description

Title :  HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN MUTANT HUMAN THIOREDOXIN AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN NFKB
 
Authors :  G. M. Clore, J. Qin, A. M. Gronenborn
Date :  27 Feb 95  (Deposition) - 03 Jun 95  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B
Keywords :  Complex (Electron Transport/Peptide) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Qin, G. M. Clore, W. M. Kennedy, J. R. Huth, A. M. Gronenborn
Solution Structure Of Human Thioredoxin In A Mixed Disulfide Intermediate Complex With Its Target Peptide From The Transcription Factor Nf Kappa B.
Structure V. 3 289 1995
PubMed-ID: 7788295  |  Reference-DOI: 10.1016/S0969-2126(01)00159-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOREDOXIN
    ChainsA
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - TARGET SITE IN HUMAN NFKB
    ChainsB
    EngineeredYES

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1MDI)

(-) Sites  (0, 0)

(no "Site" information available for 1MDI)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:32 -B:7

(-) Cis Peptide Bonds  (1, 1)

NMR Structure
No.Residues
1Thr A:74 -Pro A:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MDI)

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.THIO_HUMAN1-105  1A:1-105
2THIOREDOXIN_1PS00194 Thioredoxin family active site.THIO_HUMAN24-42  1A:24-42
3REL_1PS01204 NF-kappa-B/Rel/dorsal domain signature.NFKB1_HUMAN57-63  1B:3-9

(-) Exons   (6, 6)

NMR Structure (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003745171aENSE00001463713chr9:113018920-113018692229THIO_HUMAN1-881A:1-88
1.2ENST000003745172ENSE00000806083chr9:113013742-113013638105THIO_HUMAN9-43351A:9-4335
1.3ENST000003745173ENSE00000806082chr9:113013159-11301310060THIO_HUMAN44-63201A:44-6320
1.4bENST000003745174bENSE00000806081chr9:113007123-11300705866THIO_HUMAN64-85221A:64-8522
1.5bENST000003745175bENSE00001945358chr9:113006499-113006091409THIO_HUMAN86-105201A:86-10520

2.1bENST000003948201bENSE00002081373chr4:103422488-103422945458NFKB1_HUMAN-00--
2.5ENST000003948205ENSE00001008675chr4:103446669-10344671446NFKB1_HUMAN1-13130--
2.6ENST000003948206ENSE00000734504chr4:103450993-10345107179NFKB1_HUMAN14-40270--
2.7bENST000003948207bENSE00001519710chr4:103455005-10345504238NFKB1_HUMAN40-52130--
2.8dENST000003948208dENSE00000801437chr4:103459015-10345911399NFKB1_HUMAN53-85331B:1-1313
2.10bENST0000039482010bENSE00000801436chr4:103488144-103488292149NFKB1_HUMAN86-135500--
2.11bENST0000039482011bENSE00002185014chr4:103498033-103498196164NFKB1_HUMAN135-190560--
2.13bENST0000039482013bENSE00000801434chr4:103500038-103500196159NFKB1_HUMAN190-243540--
2.14bENST0000039482014bENSE00000801433chr4:103501692-103501796105NFKB1_HUMAN243-278360--
2.15ENST0000039482015ENSE00000801432chr4:103504023-10350411492NFKB1_HUMAN278-308310--
2.16ENST0000039482016ENSE00000801431chr4:103505839-103505977139NFKB1_HUMAN309-355470--
2.17bENST0000039482017bENSE00002163400chr4:103514582-103514725144NFKB1_HUMAN355-403490--
2.18ENST0000039482018ENSE00000734990chr4:103516049-10351613890NFKB1_HUMAN403-433310--
2.19bENST0000039482019bENSE00000801428chr4:103517295-103517489195NFKB1_HUMAN433-498660--
2.20ENST0000039482020ENSE00000801427chr4:103518677-103518818142NFKB1_HUMAN498-545480--
2.21ENST0000039482021ENSE00000801426chr4:103522052-103522166115NFKB1_HUMAN545-583390--
2.22ENST0000039482022ENSE00000801425chr4:103527653-103527854202NFKB1_HUMAN584-651680--
2.23ENST0000039482023ENSE00000801424chr4:103528307-103528476170NFKB1_HUMAN651-707570--
2.24ENST0000039482024ENSE00000735164chr4:103528806-103528908103NFKB1_HUMAN708-742350--
2.25ENST0000039482025ENSE00000735167chr4:103531732-103531856125NFKB1_HUMAN742-783420--
2.26ENST0000039482026ENSE00000801421chr4:103533201-10353326767NFKB1_HUMAN784-806230--
2.27ENST0000039482027ENSE00000735200chr4:103533591-103533763173NFKB1_HUMAN806-863580--
2.28ENST0000039482028ENSE00000801419chr4:103534582-103534738157NFKB1_HUMAN864-916530--
2.29aENST0000039482029aENSE00001519708chr4:103537591-103538072482NFKB1_HUMAN916-968530--

(-) 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:105
 aligned with THIO_HUMAN | P10599 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
           THIO_HUMAN     1 MVKQIESKTAFQEALDAAGDKLVVVDFSATWCGPCKMIKPFFHSLSEKYSNVIFLEVDVDDCQDVASECEVKCMPTFQFFKKGQKVGEFSGANKEKLEATINELV 105
               SCOP domains d1mdia_ A: Thioredoxin                                                                                    SCOP domains
               CATH domains 1mdiA00 A:1-105 Glutaredoxin                                                                              CATH domains
               Pfam domains -Thioredoxin-1mdiA01 A:2-104                                                                            - Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhh.....eeeee.....hhhhhhhhhh.hhhhh....eeeee.....hhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) THIOREDOXIN_2  PDB: A:1-105 UniProt: 1-105                                                                PROSITE (1)
                PROSITE (2) -----------------------THIOREDOXIN_1      --------------------------------------------------------------- PROSITE (2)
               Transcript 1 1.1a    Exon 1.2  PDB: A:9-43 UniProt: 9-43Exon 1.3            Exon 1.4b  PDB: A:64-8Exon 1.5b            Transcript 1
                 1mdi A   1 MVKQIESKTAFQEALDAAGDKLVVVDFSATWCGPAKMIKPFFHSLSEKYSNVIFLEVDVDDAQDVASEAEVKATPTFQFFKKGQKVGEFSGANKEKLEATINELV 105
                                    10        20        30        40        50        60        70        80        90       100     

Chain B from PDB  Type:PROTEIN  Length:13
 aligned with NFKB1_HUMAN | P19838 from UniProtKB/Swiss-Prot  Length:968

    Alignment length:13
                                    64   
          NFKB1_HUMAN    55 FRFRYVCEGPSHG  67
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains RHD-1mdiB01   Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                PROSITE (2) --REL_1  ---- PROSITE (2)
               Transcript 2 Exon 2.8d     Transcript 2
                 1mdi B   1 FRFRYVCEGPSHG  13
                                    10   

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

NMR Structure
(-)
Clan: P53-like (54)

(-) Gene Ontology  (105, 115)

NMR Structure(hide GO term definitions)
Chain A   (THIO_HUMAN | P10599)
molecular function
    GO:0016671    oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
    GO:0015037    peptide disulfide oxidoreductase activity    Catalysis of the reaction: a peptide with reduced sulfide groups = a peptide with oxidized disulfide bonds.
    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:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0032148    activation of protein kinase B activity    Any process that initiates the activity of the inactive enzyme protein kinase B.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0006662    glycerol ether metabolic process    The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
    GO:0006928    movement of cell or subcellular component    The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
    GO:1903206    negative regulation of hydrogen peroxide-induced cell death    Any process that stops, prevents or reduces the frequency, rate or extent of hydrogen peroxide-induced cell death.
    GO:0046826    negative regulation of protein export from nucleus    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of proteins from the nucleus into the cytoplasm.
    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:0015949    nucleobase-containing small molecule interconversion    The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    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: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: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:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0030091    protein repair    The process of restoring a protein to its original state after damage by such things as oxidation or spontaneous decomposition of residues.
    GO:0033158    regulation of protein import into nucleus, translocation    Any process that modulates the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009314    response to radiation    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 electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
    GO:0000302    response to reactive oxygen species    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 reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0000103    sulfate assimilation    The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO: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: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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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.

Chain B   (NFKB1_HUMAN | P19838)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000980    RNA polymerase II distal enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    GO:0042805    actinin binding    Interacting selectively and non-covalently with actinin, any member of a family of proteins that crosslink F-actin.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0031072    heat shock protein binding    Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0000975    regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0000976    transcription regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
    GO:0001205    transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0001227    transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the regulatory region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    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:0038061    NIK/NF-kappaB signaling    The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52).
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:1990416    cellular response to brain-derived neurotrophic factor stimulus    A 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 brain-derived neurotrophic factor stimulus.
    GO:0071322    cellular response to carbohydrate 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 carbohydrate stimulus.
    GO:1904630    cellular response to diterpene    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 diterpene stimulus.
    GO:0071359    cellular response to dsRNA    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 double-stranded RNA stimulus.
    GO:1904632    cellular response to glucoside    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 glucoside stimulus.
    GO:0071347    cellular response to interleukin-1    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 interleukin-1 stimulus.
    GO:0071354    cellular response to interleukin-6    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 interleukin-6 stimulus.
    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: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: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:1901653    cellular response to peptide    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 peptide stimulus.
    GO:0071375    cellular response to peptide hormone 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 peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
    GO:0071356    cellular response to tumor necrosis factor    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 tumor necrosis factor stimulus.
    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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0031293    membrane protein intracellular domain proteolysis    The proteolytic cleavage of a transmembrane protein leading to the release of an intracellular domain.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0010956    negative regulation of calcidiol 1-monooxygenase activity    Any process that decreases 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:0032269    negative regulation of cellular protein metabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
    GO:0032375    negative regulation of cholesterol transport    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of cholesterol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0001818    negative regulation of cytokine production    Any process that stops, prevents, or reduces the rate of production of a cytokine.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0045083    negative regulation of interleukin-12 biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-12.
    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:0010957    negative regulation of vitamin D biosynthetic process    Any process that decreases 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: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:0090263    positive regulation of canonical Wnt signaling pathway    Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    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:1900127    positive regulation of hyaluronan biosynthetic process    Any process that activates or increases the frequency, rate or extent of hyaluronan biosynthetic process.
    GO:0010884    positive regulation of lipid storage    Any process that increases 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:0010744    positive regulation of macrophage derived foam cell differentiation    Any process that increases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions.
    GO:2000630    positive regulation of miRNA metabolic process    Any process that activates or increases the frequency, rate or extent of miRNA metabolic process.
    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:0032481    positive regulation of type I interferon production    Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009617    response to bacterium    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 bacterium.
    GO:0046688    response to copper ion    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 copper ion stimulus.
    GO:0035994    response to muscle stretch    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 myofibril being extended beyond its slack length.
    GO:0014070    response to organic cyclic compound    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 cyclic compound stimulus.
    GO:0006979    response to oxidative 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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
    GO:0051403    stress-activated MAPK cascade    A series of molecular signals in which a stress-activated MAP kinase cascade relays one or more of the signals; MAP kinase cascades involve at least three protein kinase activities and culminate in the phosphorylation and activation of a MAP kinase.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0033256    I-kappaB/NF-kappaB complex    A protein complex containing an inhibitory-kappaB (I-kappaB/IKB) protein and one or more copies of an NF-kappaB protein. In the resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NFKB1_HUMAN | P198381mdj 1mdk 1nfi 1svc 2dbf 2o61 3gut
        THIO_HUMAN | P105991aiu 1auc 1cqg 1cqh 1ert 1eru 1erv 1erw 1m7t 1mdj 1mdk 1trs 1tru 1trv 1trw 1w1c 1w1e 2hsh 2hxk 2ifq 2iiy 3e3e 3kd0 3m9j 3m9k 3qfa 3qfb 3trx 4ll1 4ll4 4oo4 4oo5 4pok 4pol 4pom 4puf 4trx 5dqy

(-) Related Entries Specified in the PDB File

1mdj 1mdk