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(-) Description

Title :  SOLUTION STRUCTURE OF TACI-CRD2
 
Authors :  S. G. Hymowitz, D. R. Patel, H. J. Wallweber, S. Runyon, M. Yan, J. Yin, S. K. Shriver, N. C. Gordon, B. Pan, N. J. Skelton, R. F. Kelley, M. A. Starovasnik
Date :  26 Oct 04  (Deposition) - 09 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Tnf Receptor, Cytokine, Cysteine-Rich Domain, Receptor, Cytokine Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. G. Hymowitz, D. R. Patel, H. J. Wallweber, S. Runyon, M. Yan, J. Yin, S. K. Shriver, N. C. Gordon, B. Pan, N. J. Skelton, R. F. Kelley, M. A. Starovasnik
Structures Of April-Receptor Complexes: Like Bcma, Taci Employs Only A Single Cysteine-Rich Domain For High Affinity Ligand Binding.
J. Biol. Chem. V. 280 7218 2005
PubMed-ID: 15542592  |  Reference-DOI: 10.1074/JBC.M411714200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 13B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET32A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: TACI_D2
    Gene: TNFRSF13B, TACI
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRANSMEMBRANE ACTIVATOR AND CAML INTERACTOR, TNFRSF13B

 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 1XUT)

(-) Sites  (0, 0)

(no "Site" information available for 1XUT)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:71 -A:86
2A:89 -A:100
3A:93 -A:104

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024027C104RTR13B_HUMANDisease (IGAD2)34557412AC104R
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNFR_NGFR_1PS00652 TNFR/NGFR family cysteine-rich region signature.TR13B_HUMAN34-71  1A:66-71

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002616521ENSE00001378434chr17:16875402-1687532974TR13B_HUMAN1-21210--
1.2ENST000002616522ENSE00001309090chr17:16855897-16855760138TR13B_HUMAN21-67471A:64-67 (gaps)8
1.3ENST000002616523ENSE00001151854chr17:16852297-16852052246TR13B_HUMAN67-149831A:68-10942
1.4ENST000002616524ENSE00000691547chr17:16843825-16843640186TR13B_HUMAN149-211630--
1.5bENST000002616525bENSE00001323387chr17:16843111-16842399713TR13B_HUMAN211-293830--

(-) 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:46
 aligned with TR13B_HUMAN | O14836 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:77
                                    42        52        62        72        82        92       102       
          TR13B_HUMAN    33 SCPEEQYWDPLLGTCMSCKTICNHQSQRTCAAFCRSLSCRKEQGKFYDHLLRDCISCASICGQHPKQCAYFCENKLR 109
               SCOP domains d1x    u                           ta_ A:                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------TACI-CRD2-1xutA01 A:69-109                Pfam domains (1)
           Pfam domains (2) ------------------------------------TACI-CRD2-1xutA02 A:69-109                Pfam domains (2)
         Sec.struct. author ...----.---------------------------.........eeee....eeee.........hhhhhh...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------R----- SAPs(SNPs)
                    PROSITE -TNFR_NGFR_1  PDB: A:66-71             -------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:64-67 (gaps)      ------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3  PDB: A:68-109 UniProt: 67-149     Transcript 1 (2)
                 1xut A  64 GSP----W---------------------------SLSCRKEQGKFYDHLLRDCISCASICGQHPKQCAYFCENKLR 109
                              |    | -         -         -     |  72        82        92       102       
                             66   67                          68
   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: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XUT)

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: no clan defined [family: TACI-CRD2] (2)

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain A   (TR13B_HUMAN | O14836)
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.
biological process
    GO:0001782    B cell homeostasis    The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    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:0002244    hematopoietic progenitor cell differentiation    The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
    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:0030889    negative regulation of B cell proliferation    Any process that stops, prevents or reduces the rate or extent of B cell proliferation.
    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:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        TR13B_HUMAN | O14836: 1xu1

(-) Related Entries Specified in the PDB File

1xu1 CRYSTAL STRUCTURE OF APRIL BOUND TO TACI
1xu2