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(-) Description

Title :  STRUCTURE OF BHPBR3, THE BAFF-BINDING LOOP OF BR3 EMBEDDED IN A BETA-HAIRPIN PEPTIDE
 
Authors :  N. Kayagaki, M. Yan, D. Seshasayee, H. Wang, W. Lee, D. M. French, I. S. Grewal, A. G. Cochran, N. C. Gordon, J. Yin, M. A. Starovasnik, V. M. Dixit
Date :  12 Sep 02  (Deposition) - 30 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Beta-Hairpin, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Kayagaki, M. Yan, D. Seshasayee, H. Wang, W. Lee, D. M. French, I. S. Grewal, A. G. Cochran, N. C. Gordon, J. Yin, M. A. Starovasnik, V. M. Dixit
Baff/Blys Receptor 3 Binds The B Cell Survival Factor Baff Ligand Through A Discrete Surface Loop And Promotes Processing Of Nf-Kappab2.
Immunity V. 17 515 2002
PubMed-ID: 12387744  |  Reference-DOI: 10.1016/S1074-7613(02)00425-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BLYS RECEPTOR 3
    ChainsA
    EngineeredYES
    FragmentBR3 LOOP (RESIDUES 26-31)
    Other DetailsTHE RECEPTOR LOOP IS EMBEDDED WITHIN A BETA- HAIRPIN (BHP) SCAFFOLD
    Other Details - SourceTHE PEPTIDE WAS SYNTHESIZED CHEMICALLY WITH ACETYLATED N-TERMINUS AND AMIDATED C-TERMINUS
    SynonymTUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 13C, B CELL-ACTIVATING FACTOR RECEPTOR, BAFF RECEPTOR, BAFF-R, BLYS RECEPTOR 3
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

NMR Structure (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:24 , VAL A:33BINDING SITE FOR RESIDUE ACE A 22
2AC2SOFTWARECYS A:34BINDING SITE FOR RESIDUE NH2 A 35

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:23 -A:34

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MPV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MPV)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002912321ENSE00001175504chr22:42322822-42322642181TR13C_HUMAN1-46461A:22-35 (gaps)19
1.2ENST000002912322ENSE00001048605chr22:42322335-42322105231TR13C_HUMAN46-123780--
1.3ENST000002912323ENSE00001201908chr22:42321558-42321045514TR13C_HUMAN123-184620--

(-) 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:14
 aligned with TR13C_HUMAN | Q96RJ3 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:19
                                    27         
           TR13C_HUMAN   18 PCVPAECFDLLVRHCVACG 36
               SCOP domains d1m    pva_ A:      SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ..e----ee....eee-.. Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
               Transcript 1 Exon 1.1            Transcript 1
                  1mpv A 22 xCH----WDLLVRHWV-Cx 35
                            | |    |27     | ||
                            | |   25      33 ||
                           22-ACE           34|
                             24              35-NH2

   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  (1, 1)

NMR Structure
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1MPV)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (TR13C_HUMAN | Q96RJ3)
biological process
    GO:0031296    B cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the B cell receptor to augment B cell activation.
    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:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    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: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:0030890    positive regulation of B cell proliferation    Any process that activates or increases the rate or extent of B cell proliferation.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0002636    positive regulation of germinal center formation    Any process that activates or increases the frequency, rate, or extent of germinal center formation.
    GO:0045078    positive regulation of interferon-gamma biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interferon-gamma.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    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: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
        TR13C_HUMAN | Q96RJ31oqe 1osx 2hfg 3v56 4v46

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