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PDBsum entry 1oqe

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protein Protein-protein interface(s) links
Immune system PDB id
1oqe
Jmol
Contents
Protein chains
(+ 4 more) 144 a.a. *
(+ 1 more) 31 a.a. *
24 a.a. *
* Residue conservation analysis
PDB id:
1oqe
Name: Immune system
Title: Crystal structure of stall-1 with baff-r
Structure: Tumor necrosis factor ligand superfamily member 13b, soluble form. Chain: a, b, c, d, e, f, g, h, i, j. Fragment: extracellular domain. Synonym: tnf-and apol- related leukocyte expressed ligand 1, tall-1, b lymphocyte stimulator, blys, b cell- activating factor, baff, dendritic cell- derived tnf-like molecule. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Hexamer (from PDB file)
Resolution:
2.50Å     R-factor:   0.244     R-free:   0.259
Authors: G.Zhang
Key ref:
Y.Liu et al. (2003). Ligand-receptor binding revealed by the TNF family member TALL-1. Nature, 423, 49-56. PubMed id: 12721620 DOI: 10.1038/nature01543
Date:
07-Mar-03     Release date:   13-May-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9Y275  (TN13B_HUMAN) -  Tumor necrosis factor ligand superfamily member 13B
Seq:
Struc:
285 a.a.
144 a.a.
Protein chains
Pfam   ArchSchema ?
Q96RJ3  (TR13C_HUMAN) -  Tumor necrosis factor receptor superfamily member 13C
Seq:
Struc:
184 a.a.
31 a.a.
Protein chain
Pfam   ArchSchema ?
Q96RJ3  (TR13C_HUMAN) -  Tumor necrosis factor receptor superfamily member 13C
Seq:
Struc:
184 a.a.
24 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     immune response   1 term 
  Biochemical function     tumor necrosis factor receptor binding     1 term  

 

 
DOI no: 10.1038/nature01543 Nature 423:49-56 (2003)
PubMed id: 12721620  
 
 
Ligand-receptor binding revealed by the TNF family member TALL-1.
Y.Liu, X.Hong, J.Kappler, L.Jiang, R.Zhang, L.Xu, C.H.Pan, W.E.Martin, R.C.Murphy, H.B.Shu, S.Dai, G.Zhang.
 
  ABSTRACT  
 
The tumour necrosis factor (TNF) ligand TALL-1 and its cognate receptors, BCMA, TACI and BAFF-R, were recently identified as members of the TNF superfamily, which are essential factors contributing to B-cell maturation. The functional, soluble fragment of TALL-1 (sTALL-1) forms a virus-like assembly for its proper function. Here we determine the crystal structures of sTALL-1 complexed with the extracellular domains of BCMA and BAFF-R at 2.6 and 2.5 A, respectively. The single cysteine-rich domain of BCMA and BAFF-R both have saddle-like architectures, which sit on the horseback-like surface formed by four coil regions on each individual sTALL-1 monomer. Three novel structural modules, D2, X2 and N, were revealed from the current structures. Sequence alignments, structural modelling and mutagenesis revealed that one disulphide bridge in BAFF-R is critical for determining the binding specificity of the extracellular domain eBAFF-R to TALL-1 instead of APRIL, a closely related ligand of TALL-1, which was confirmed by binding experiments in vitro.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Structures of eBCMA and eBAFF-R. a, Initial F[o] - F[c] map of eBCMA with sTALL-1 at the 2.5 level. Phases are calculated from the sTALL-1 model (Protein Data Bank ID 1JH5). eBCMA is shown as the final refined model. The portion of the map shown is representative of all eight bound receptors in the asymmetric unit. Most residues are shown with their side chains. b, Ribbon diagram of the three-dimensional structure of eBCMA (residues 5 -43), showing three disulphide bridges. c, Ribbon diagram of the three-dimensional structure of eBAFF-R (residues 16 -45), showing two disulphide bridges. All figures were prepared with RIBBONS44 except a, which was prepared with BOBSCRIPT45.
Figure 4.
Figure 4: Detailed interactions of the two complexes. a -f, Interactions between eBCMA and sTALL1: a, the one-to-one interaction mode of eBCMA with sTALL-1; b, two trimers of the complex of eBCMA and sTALL-1; c, the overall interactions between eBCMA and sTALL-1; d, hydrophobic core 1 between eBCMA and sTALL-1; e, hydrophobic core 2 between eBCMA and sTALL-1; f, salt bridges 1 and 2 in the complex of eBCMA and sTALL-1. g -i, Interactions between eBAFF-R and sTALL-1: g, hydrophobic core 1 between eBAFF-R and sTALL-1; h, hydrophobic core 2 between eBAFF-R and sTALL-1; i, hydrogen bonds and salt bridges in the extended coil region of eBAFF-R with sTALL-1.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2003, 423, 49-56) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20636814 R.Elgueta, V.C.de Vries, and R.J.Noelle (2010).
The immortality of humoral immunity.
  Immunol Rev, 236, 139-150.  
19241374 F.He, W.Dang, K.Saito, S.Watanabe, N.Kobayashi, P.Güntert, T.Kigawa, A.Tanaka, Y.Muto, and S.Yokoyama (2009).
Solution structure of the cysteine-rich domain in Fn14, a member of the tumor necrosis factor receptor superfamily.
  Protein Sci, 18, 650-656.
PDB code: 2rpj
19521398 F.Mackay, and P.Schneider (2009).
Cracking the BAFF code.
  Nat Rev Immunol, 9, 491-502.  
17942754 C.Bossen, T.G.Cachero, A.Tardivel, K.Ingold, L.Willen, M.Dobles, M.L.Scott, A.Maquelin, E.Belnoue, C.A.Siegrist, S.Chevrier, H.Acha-Orbea, H.Leung, F.Mackay, J.Tschopp, and P.Schneider (2008).
TACI, unlike BAFF-R, is solely activated by oligomeric BAFF and APRIL to support survival of activated B cells and plasmablasts.
  Blood, 111, 1004-1012.  
18378892 Z.Zhou, X.Song, A.Berezov, G.Zhang, Y.Li, H.Zhang, R.Murali, B.Li, and M.I.Greene (2008).
Human glucocorticoid-induced TNF receptor ligand regulates its signaling activity through multiple oligomerization states.
  Proc Natl Acad Sci U S A, 105, 5465-5470.  
16547002 C.Bossen, K.Ingold, A.Tardivel, J.L.Bodmer, O.Gaide, S.Hertig, C.Ambrose, J.Tschopp, and P.Schneider (2006).
Interactions of tumor necrosis factor (TNF) and TNF receptor family members in the mouse and human.
  J Biol Chem, 281, 13964-13971.  
16914324 C.Bossen, and P.Schneider (2006).
BAFF, APRIL and their receptors: structure, function and signaling.
  Semin Immunol, 18, 263-275.  
16557636 L.L.Kiessling, J.E.Gestwicki, and L.E.Strong (2006).
Synthetic multivalent ligands as probes of signal transduction.
  Angew Chem Int Ed Engl, 45, 2348-2368.  
16474316 S.R.Dillon, J.A.Gross, S.M.Ansell, and A.J.Novak (2006).
An APRIL to remember: novel TNF ligands as therapeutic targets.
  Nat Rev Drug Discov, 5, 235-246.  
16255842 M.Cao, L.Chen, X.X.Shan, and S.Q.Zhang (2005).
Immunological effects of refolded human soluble BAFF synthesized in Escherichia coli on murine B lymphocytes in vitro and in vivo.
  Jpn J Physiol, 55, 221-227.  
15886118 P.Schneider (2005).
The role of APRIL and BAFF in lymphocyte activation.
  Curr Opin Immunol, 17, 282-289.  
15549676 R.L.Rich, and D.G.Myszka (2005).
Survey of the year 2003 commercial optical biosensor literature.
  J Mol Recognit, 18, 1.  
16370373 S.Fournel, S.Wieckowski, W.Sun, N.Trouche, H.Dumortier, A.Bianco, O.Chaloin, M.Habib, J.C.Peter, P.Schneider, B.Vray, R.E.Toes, R.Offringa, C.J.Melief, J.Hoebeke, and G.Guichard (2005).
C3-symmetric peptide scaffolds are functional mimetics of trimeric CD40L.
  Nat Chem Biol, 1, 377-382.  
15542592 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, and M.A.Starovasnik (2005).
Structures of APRIL-receptor complexes: like BCMA, TACI employs only a single cysteine-rich domain for high affinity ligand binding.
  J Biol Chem, 280, 7218-7227.
PDB codes: 1xu1 1xu2 1xut
14764606 D.R.Patel, H.J.Wallweber, J.Yin, S.K.Shriver, S.A.Marsters, N.C.Gordon, M.A.Starovasnik, and R.F.Kelley (2004).
Engineering an APRIL-specific B cell maturation antigen.
  J Biol Chem, 279, 16727-16735.  
15093829 G.Zhang (2004).
Tumor necrosis factor family ligand-receptor binding.
  Curr Opin Struct Biol, 14, 154-160.  
15288003 K.P.Baker (2004).
BLyS--an essential survival factor for B cells: basic biology, links to pathology and therapeutic target.
  Autoimmun Rev, 3, 368-375.  
15546397 M.P.Cancro (2004).
The BLyS family of ligands and receptors: an archetype for niche-specific homeostatic regulation.
  Immunol Rev, 202, 237-249.  
15161425 W.Stohl (2004).
Targeting B lymphocyte stimulator in systemic lupus erythematosus and other autoimmune rheumatic disorders.
  Expert Opin Ther Targets, 8, 177-189.  
12867412 A.L.Gavin, D.Aït-Azzouzene, C.F.Ware, and D.Nemazee (2003).
DeltaBAFF, an alternate splice isoform that regulates receptor binding and biopresentation of the B cell survival cytokine, BAFF.
  J Biol Chem, 278, 38220-38228.  
12787568 F.Mackay, and C.Ambrose (2003).
The TNF family members BAFF and APRIL: the growing complexity.
  Cytokine Growth Factor Rev, 14, 311-324.  
12796483 M.Pelletier, J.S.Thompson, F.Qian, S.A.Bixler, D.Gong, T.Cachero, K.Gilbride, E.Day, M.Zafari, C.Benjamin, L.Gorelik, A.Whitty, S.L.Kalled, C.Ambrose, and Y.M.Hsu (2003).
Comparison of soluble decoy IgG fusion proteins of BAFF-R and BCMA as antagonists for BAFF.
  J Biol Chem, 278, 33127-33133.  
14656435 S.G.Hymowitz, D.M.Compaan, M.Yan, H.J.Wallweber, V.M.Dixit, M.A.Starovasnik, and A.M.de Vos (2003).
The crystal structures of EDA-A1 and EDA-A2: splice variants with distinct receptor specificity.
  Structure, 11, 1513-1520.
PDB codes: 1rj7 1rj8
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.