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(-) Description

Title :  SOLUTION STRUCTURE OF THE CIDE-N DOMAIN OF HUMAN CELL DEATH ACTIVATOR CIDE-A
 
Authors :  X. R. Qin, T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 Feb 07  (Deposition) - 21 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Cide-N Domain, Cell Death Activator Cide-A, Cell Death- Inducing Dffa-Like Effector A, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. R. Qin, T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of The Cide-N Domain Of Human Cell Death Activator Cide-A
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CELL DEATH ACTIVATOR CIDE-A
    ChainsA
    EngineeredYES
    Expression System PlasmidP050613-03
    Expression System Vector TypePLASMID
    FragmentCIDE-N DOMAIN
    GeneCIDEA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymCELL DEATH-INDUCING DFFA-LIKE EFFECTOR A

 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 2EEL)

(-) Sites  (0, 0)

(no "Site" information available for 2EEL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CIDE_NPS51135 CIDE-N domain profile.CIDEA_HUMAN33-110  1A:8-85

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003204771aENSE00001261168chr18:12254318-12254420103CIDEA_HUMAN1-13130--
1.2ENST000003204772ENSE00001261135chr18:12262824-12262968145CIDEA_HUMAN13-61491A:1-36 (gaps)43
1.4ENST000003204774ENSE00001261131chr18:12264306-12264452147CIDEA_HUMAN62-110491A:37-8549
1.5ENST000003204775ENSE00001261125chr18:12274092-12274273182CIDEA_HUMAN111-171611A:86-91 (gaps)7
1.6aENST000003204776aENSE00001855893chr18:12277122-12277279158CIDEA_HUMAN171-219490--

(-) 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 CIDEA_HUMAN | O60543 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:107
                                    28        38        48        58        68        78        88        98       108       118       
          CIDEA_HUMAN    19 GSQTKRVLFTPLMHPARPFRVSNHDRSSRRGVMASSLQELISKTLDALVIATGLVTLVLEEDGTVVDTEEFFQTLGDNTHFMILEKGQKWMPGSQHVPTCSPPKRSG 125
               SCOP domains d2eel       a_ A: automated matches                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-------....eeeeee.......eeeee.hhhhhhhhhhhhh......eeeee........hhhhhh.....eeeeeee.......--------....-.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------CIDE_N  PDB: A:8-85 UniProt: 33-110                                           --------------- PROSITE
               Transcript 1 Exon 1.2  PDB: A:1-36 (gaps) UniProt: 13-61Exon 1.4  PDB: A:37-85 UniProt: 62-110           Exon 1.5        Transcript 1
                 2eel A   1 GSSGS-------SGPARPFRVSNHDRSSRRGVMASSLQELISKTLDALVIATGLVTLVLEEDGTVVDTEEFFQTLGDNTHFMILEKGQKWMP--------SGPS-SG  91
                                |    -  |     13        23        33        43        53        63        73        83 |       -|  | | 
                                5       6                                                                             85       86 89 | 
                                                                                                                                    90 

   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (CIDEA_HUMAN | O60543)
molecular function
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
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:0008219    cell death    Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0019915    lipid storage    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:0050710    negative regulation of cytokine secretion    Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of cytokines from a cell.
    GO:1900118    negative regulation of execution phase of apoptosis    Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis.
    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:0030512    negative regulation of transforming growth factor beta receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway.
    GO:0032720    negative regulation of tumor necrosis factor production    Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production.
    GO:0010890    positive regulation of sequestering of triglyceride    Any process that increases the rate, frequency or extent of sequestering of triglyceride. Triglyceride sequestration is the process of binding or confining any triester of glycerol such that it is separated from other components of a biological system.
    GO:1902510    regulation of apoptotic DNA fragmentation    Any process that modulates the frequency, rate or extent of apoptotic DNA fragmentation.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0035634    response to stilbenoid    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 exposure to a stilbenoid. Stilbenoids are secondary products of heartwood formation in trees that can act as phytoalexins. Stilbenoids are hydroxylated derivatives of stilbene. They belong to the family of phenylpropanoids and share most of their biosynthesis pathway with chalcones.
    GO:0001659    temperature homeostasis    A homeostatic process in which an organism modulates its internal body temperature.
    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: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:0005811    lipid droplet    An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
    GO:0005740    mitochondrial envelope    The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.
    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: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.

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