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(-) Description

Title :  CRYSTAL STRUCTURE OF DCR3
 
Authors :  C. Zhan, Y. Patskovsky, Q. Yan, Z. Li, U. A. Ramagopal, S. G. Nathenson, S
Date :  07 Apr 10  (Deposition) - 23 Feb 11  (Release) - 23 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  D
Keywords :  Dcr3, Tnfr, Decoy Receptor, Glycoprotein, Secreted, Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Zhan, Y. Patskovsky, Q. Yan, Z. Li, U. Ramagopal, H. Cheng, M. Brenowitz, X. Hui, S. G. Nathenson, S. C. Almo
Decoy Strategies: The Structure Of Tl1A:Dcr3 Complex.
Structure V. 19 162 2011
PubMed-ID: 21300286  |  Reference-DOI: 10.1016/J.STR.2010.12.004

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 6B
    ChainsD
    EngineeredYES
    Expression SystemDROSOPHILA
    Expression System Cell LineS2
    Expression System PlasmidPMT/BIP/V5-HIS
    Expression System Taxid7215
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 30-195
    GeneDCR3, TNFRSF6B, TR6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDECOY RECEPTOR FOR FAS LIGAND, DECOY RECEPTOR 3, DCR3, M68

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3MHD)

(-) Sites  (0, 0)

(no "Site" information available for 3MHD)

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1D:49 -D:62
2D:52 -D:70
3D:73 -D:88
4D:91 -D:105
5D:95 -D:113
6D:115 -D:126
7D:132 -D:150

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MHD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MHD)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNFR_NGFR_1PS00652 TNFR/NGFR family cysteine-rich region signature.TNF6B_HUMAN70-113  1D:70-113
2TNFR_NGFR_2PS50050 TNFR/NGFR family cysteine-rich region domain profile.TNF6B_HUMAN72-113
152-193
  2D:72-113
D:157-167

(-) Exons   (0, 0)

(no "Exon" information available for 3MHD)

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain D from PDB  Type:PROTEIN  Length:130
 aligned with TNF6B_HUMAN | O95407 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:136
                                    41        51        61        71        81        91       101       111       121       131       141       151       161      
          TNF6B_HUMAN    32 ETPTYPWRDAETGERLVCAQCPPGTFVQRPCRRDSPTTCGPCPPRHYTQFWNYLERCRYCNVLCGEREEEARACHATHNRACRCRTGFFAHAGFCLEHASCPPGAGVIAPGTPSQNTQCQPCPPGTFSASSSSSEQ 167
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------TNFR_c6-3mhdD01 D:73-113                 ------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee......eeeee.....eeeee........eeee....ee..........ee........eeeee........eeee...eee....eee......................------........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------TNFR_NGFR_1  PDB: D:70-113 UniProt: 70-113  --------------------------------------TNFR_NGFR_2      PROSITE (1)
                PROSITE (2) ----------------------------------------TNFR_NGFR_2  PDB: D:72-113 UniProt: 72-113------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mhd D  32 ETPTYPWRDAETGERLVCAQCPPGTFVQRPCRRDSPTTCGPCPPRHYTQFWNYLERCRYCNVLCGEREEEARACHATHNRACRCRTGFFAHAGFCLEHASCPPGAGVIAPGTPSQNTQC------TFSASSSSSEQ 167
                                    41        51        61        71        81        91       101       111       121       131       141        |-     | 161      
                                                                                                                                                150    157          

   Legend:   → Mismatch (orange background)
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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 3MHD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MHD)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain D   (TNF6B_HUMAN | O95407)
molecular function
    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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    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: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:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    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:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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: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:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    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: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: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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TNF6B_HUMAN | O954073k51 3mi8 4j6g 4kgg 4kgq 4msv 5l36

(-) Related Entries Specified in the PDB File

2qe3 CRYSTAL STRUCTURE OF TL1A
3k51 CRYSTAL STRUCTURE OF TL1A-DCR3 COMPLEX
3mi8