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(-) Description

Title :  CRYSTAL STRUCTURE OF RAIDD DD
 
Authors :  H. Wu, H. Park
Date :  09 Dec 06  (Deposition) - 30 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Raidd, Death Domain, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. H. Park, H. Wu
Crystal Structure Of Raidd Death Domain Implicates Potential Mechanism Of Piddosome Assembly
J. Mol. Biol. V. 357 358 2006
PubMed-ID: 16434054  |  Reference-DOI: 10.1016/J.JMB.2005.12.082
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEATH DOMAIN-CONTAINING PROTEIN CRADD
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET 26B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentDEATH DOMAIN, RESIDUES 95-199
    GeneCRADD, RAIDD
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCASPASE AND RIP ADAPTER WITH DEATH DOMAIN, RIP- ASSOCIATED PROTEIN WITH A DEATH DOMAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2O71)

(-) Sites  (0, 0)

(no "Site" information available for 2O71)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O71)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O71)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_067536G128RCRADD_HUMANDisease (MRT34)387906861AG128R

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEATH_DOMAINPS50017 Death domain profile.CRADD_HUMAN116-188  1A:116-188

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003328961ENSE00001274256chr12:94071151-9407124898CRADD_HUMAN-00--
1.2ENST000003328962ENSE00001155225chr12:94072545-94072848304CRADD_HUMAN1-1001000--
1.3ENST000003328963ENSE00001274268chr12:94243746-94244527782CRADD_HUMAN100-1991001A:109-19991

(-) 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 A from PDB  Type:PROTEIN  Length:91
 aligned with CRADD_HUMAN | P78560 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:91
                                   118       128       138       148       158       168       178       188       198 
          CRADD_HUMAN   109 HILNSSPSDRQINQLAQRLGPEWEPMVLSLGLSQTDIYRCKANHPHNVQSQVVEAFIRWRQRFGKQATFQSLHNGLRAVEVDPSLLLHMLE 199
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------Death-2o71A01 A:117-194                                                       ----- Pfam domains
         Sec.struct. author hhhhh..hhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------R----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------DEATH_DOMAIN  PDB: A:116-188 UniProt: 116-188                            ----------- PROSITE
               Transcript 1 Exon 1.3  PDB: A:109-199 UniProt: 100-199 [INCOMPLETE]                                      Transcript 1
                 2o71 A 109 HILNSSPSDRQINQLAQRLGPEWEPMVLSLGLSQTDIYRCKANHPHNVQSQVVEAFIRWRQRFGKQATFQSLHNGLRAVEVDPSLLLHMLE 199
                                   118       128       138       148       158       168       178       188       198 

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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  (0, 0)

(no "SCOP Domain" information available for 2O71)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O71)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Death (18)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CRADD_HUMAN | P78560)
molecular function
    GO:0070513    death domain binding    Interacting selectively and non-covalently with a death domain of a protein. The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD bind each other forming oligomers. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB.
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
biological process
    GO:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    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: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: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: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:2001235    positive regulation of apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    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.
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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        CRADD_HUMAN | P785602of5 3crd

(-) Related Entries Specified in the PDB File

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