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(-) Description

Title :  SOLUTION STRUCTURE OF P45 DEATH DOMAIN
 
Authors :  M. Vilar, T. C. Sung, K. F. Lee, R. Riek
Date :  08 Sep 06  (Deposition) - 23 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  P45, Death Domain, Apoptosis, P75, Nogo, Fadd (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Vilar, T. C. Sung, K. F. Lee, R. Riek
Solution Structure Of P45 Death Domain
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEATH DOMAIN CONTAINING MEMBRANE PROTEIN NRADD
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX2T
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 138-228
    GeneNRADD
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymNEUROTROPHIN RECEPTOR ASSOCIATED DEATH DOMAIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2IB1)

(-) Sites  (0, 0)

(no "Site" information available for 2IB1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IB1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IB1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IB1)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEATH_DOMAINPS50017 Death domain profile.NRADD_MOUSE158-222  1A:158-222

(-) Exons   (0, 0)

(no "Exon" information available for 2IB1)

(-) 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:91
 aligned with NRADD_MOUSE | Q8CJ26 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:91
                                   147       157       167       177       187       197       207       217       227 
          NRADD_MOUSE   138 PQQQQEEVQRLLMMGEPAKGWQELAGHLGYQAEAVETMACDQMPAYTLLRNWAAQEGNRATLRVLEDALAAIGREDVVQVLSSPAESSSVV 228
               SCOP domains d2ib1a_ A: automated matches                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhh...hhhhhhhhhh..........hhhhhhhhh..hhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------DEATH_DOMAIN  PDB: A:158-222 UniProt: 158-222                    ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 2ib1 A 138 PQQQQEEVQRLLMMGEPAKGWQELAGHLGYQAEAVETMACDQMPAYTLLRNWAAQEGNRATLRVLEDALAAIGREDVVQVLSSPAESSSVV 228
                                   147       157       167       177       187       197       207       217       227 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "CATH Domain" information available for 2IB1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IB1)

(-) Gene Ontology  (26, 26)

NMR Structure(hide GO term definitions)
Chain A   (NRADD_MOUSE | Q8CJ26)
molecular function
    GO:0005166    neurotrophin p75 receptor binding    Interacting selectively and non-covalently with the neurotrophin p75 receptor.
    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:0005031    tumor necrosis factor-activated receptor activity    Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function.
biological process
    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:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    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:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    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:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:0010942    positive regulation of cell death    Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0043281    regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that modulates the activity of a cysteine-type endopeptidase involved in apoptosis.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO: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: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:0044298    cell body membrane    The plasma membrane of a cell that bears surface projections such as axons, dendrites, cilia, or flagella, excluding the plasma membrane on cell projections.
    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:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0032589    neuron projection membrane    The portion of the plasma membrane surrounding a neuron projection.
    GO:0005641    nuclear envelope lumen    The region between the two lipid bilayers of the nuclear envelope; 20-40 nm wide.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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