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(-) Description

Title :  FADD DEATH EFFECTOR DOMAIN, F25Y MUTANT, NMR MINIMIZED AVERAGE STRUCTURE
 
Authors :  M. Eberstadt, B. Huang, Z. Chen, R. P. Meadows, C. Ng, S. W. Fesik
Date :  18 Dec 97  (Deposition) - 30 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Apoptosis, Death Effector Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Eberstadt, B. Huang, Z. Chen, R. P. Meadows, S. C. Ng, L. Zheng, M. J. Lenardo, S. W. Fesik
Nmr Structure And Mutagenesis Of The Fadd (Mort1) Death-Effector Domain.
Nature V. 392 941 1998
PubMed-ID: 9582077  |  Reference-DOI: 10.1038/31972
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FADD PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: HMS174 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PROKARYOTIC
    Fragment: DEATH EFFECTOR DOMAIN
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SYNTHETIC GENE
    Synonym: FAS-ASSOCIATING DEATH DOMAIN-CONTAINING PROTEIN

 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 1A1W)

(-) Sites  (0, 0)

(no "Site" information available for 1A1W)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1A1W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1A1W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A1W)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEDPS50168 Death effector domain (DED) profile.FADD_HUMAN3-81  1A:3-81

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003018381ENSE00001119659chr11:70049269-70049851583FADD_HUMAN1-96961A:1-8383
1.2ENST000003018382ENSE00001119658chr11:70052239-700534961258FADD_HUMAN96-2081130--

(-) 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:83
 aligned with FADD_HUMAN | Q13158 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:83
                                    10        20        30        40        50        60        70        80   
            FADD_HUMAN    1 MDPFLVLLHSVSSSLSSSELTELKFLCLGRVGKRKLERVQSGLDLFSMLLEQNDLEPGHTELLRELLASLRRHDLLRRVDDFE 83
               SCOP domains d1a1wa_ A: FADD (Mort1)                                                             SCOP domains
               CATH domains 1a1wA00 A:1-83 Death Domain, Fas                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhh....hhhhhhhhh.........hhhhhhhhhh...hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --DED  PDB: A:3-81 UniProt: 3-81                                                 -- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-83 UniProt: 1-96 [INCOMPLETE]                                    Transcript 1
                  1a1w A  1 MDPFLVLLHSVSSSLSSSELTELKYLCLGRVGKRKLERVQSGLDLFSMLLEQNDLEPGHTELLRELLASLRRHDLLRRVDDFE 83
                                    10        20        30        40        50        60        70        80
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A1W)

(-) Gene Ontology  (65, 65)

NMR Structure(hide GO term definitions)
Chain A   (FADD_HUMAN | Q13158)
molecular function
    GO:0089720    caspase binding    Interacting selectively and non-covalently with a caspase family protein.
    GO:0035877    death effector domain binding    Interacting selectively and non-covalently with a DED domain (death effector domain) of a protein, a homotypic protein interaction module composed of a bundle of six alpha-helices that is related in structure to the death domain (DD).
    GO:0005123    death receptor binding    Interacting selectively and non-covalently with any member of the death receptor (DR) family. The DR family falls within the tumor necrosis factor receptor superfamily and is characterized by a cytoplasmic region of ~80 residues termed the death domain (DD).
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005164    tumor necrosis factor receptor binding    Interacting selectively and non-covalently with the tumor necrosis factor receptor.
    GO:0032813    tumor necrosis factor receptor superfamily binding    Interacting selectively and non-covalently with any member of the tumor necrosis factor receptor superfamily.
biological process
    GO:0033077    T cell differentiation in thymus    The process in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus.
    GO:0043029    T cell homeostasis    The process of regulating the proliferation and elimination of T cells such that the total number of T cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    GO:0036462    TRAIL-activated apoptotic signaling pathway    An extrinsic apoptotic signaling pathway initiated by the binding of the ligand TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) to a death receptor on the cell surface.
    GO:0035666    TRIF-dependent toll-like receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the TRIF adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
    GO:0097202    activation of cysteine-type endopeptidase activity    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase.
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0097296    activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway    Any process that initiates the activity of an inactive cysteine-type endopeptidase involved in the apoptotic signaling pathway.
    GO: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: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:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    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: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:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    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: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: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:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0048535    lymph node development    The process whose specific outcome is the progression of lymph nodes over time, from their formation to the mature structure. A lymph node is a round, oval, or bean shaped structure localized in clusters along the lymphatic vessels, with a distinct internal structure including specialized vasculature and B- and T-zones for the activation of lymphocytes.
    GO:0097049    motor neuron apoptotic process    Any apoptotic process in a motor neuron, an efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement.
    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:0070236    negative regulation of activation-induced cell death of T cells    Any process that stops, prevents, or reduces the frequency, rate or extent of activation-induced cell death of T cells.
    GO:1902042    negative regulation of extrinsic apoptotic signaling pathway via death domain receptors    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
    GO:0060546    negative regulation of necroptotic process    Any process that decreases the rate, frequency or extent of a necroptotic process, a necrotic cell death process that results from the activation of endogenous cellular processes, such as signaling involving death domain receptors or Toll-like receptors.
    GO:2000454    positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation    Any process that activates or increases the frequency, rate or extent of CD8-positive, alpha-beta cytotoxic T cell extravasation.
    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:0001916    positive regulation of T cell mediated cytotoxicity    Any process that activates or increases the frequency, rate or extent of T cell mediated cytotoxicity.
    GO:0042104    positive regulation of activated T cell proliferation    Any process that activates or increases the rate or extent of activated T cell proliferation.
    GO:0002821    positive regulation of adaptive immune response    Any process that activates or increases the frequency, rate, or extent of an adaptive immune response.
    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:2001238    positive regulation of extrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway.
    GO:1902043    positive regulation of extrinsic apoptotic signaling pathway via death domain receptors    Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
    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:0032757    positive regulation of interleukin-8 production    Any process that activates or increases the frequency, rate, or extent of interleukin-8 production.
    GO:0045651    positive regulation of macrophage differentiation    Any process that activates or increases the frequency, rate or extent of macrophage differentiation.
    GO:0045862    positive regulation of proteolysis    Any process that activates or increases the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0032760    positive regulation of tumor necrosis factor production    Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
    GO:0060340    positive regulation of type I interferon-mediated signaling pathway    Any process that increases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
    GO:0051291    protein heterooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:1902041    regulation of extrinsic apoptotic signaling pathway via death domain receptors    Any process that modulates the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
    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:0048536    spleen development    The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
    GO:0048538    thymus development    The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0031265    CD95 death-inducing signaling complex    A protein complex formed upon binding of Fas/CD95/APO-1 to its ligand. The complex includes FADD/Mort1, procaspase-8/10 and c-FLIP in addition to the ligand-bound receptor.
    GO:0044297    cell body    The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
    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:0031264    death-inducing signaling complex    A protein complex formed by the association of signaling proteins with a death receptor upon ligand binding. The complex includes procaspases and death domain-containing proteins in addition to the ligand-bound receptor, and may control the activation of caspases 8 and 10.
    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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0097342    ripoptosome    A protein complex whose core components are the receptor-interacting serine/threonine-protein kinases RIPK1 and RIPK3 (also called RIP1 and RIP3). Formation of the ripoptosome can induce an extrinsic apoptotic signaling pathway or a necroptotic signaling pathway. The composition of this protein complex may depend on several factors including nature of the signal, cell type and more.

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        FADD_HUMAN | Q13158: 1a1z 1e3y 1e41 2gf5 3ezq 3oq9

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