PDBsum entry 1rf3

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protein Protein-protein interface(s) links
Signaling protein PDB id
Protein chains
192 a.a. *
24 a.a. *
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Structurally distinct recognition motifs in lymphotoxin-b receptor and cd40 for traf-mediated signaling
Structure: Tnf receptor associated factor 3. Chain: a. Fragment: recognition motif (residues 377-568). Synonym: cd40 receptor associated factor 1, craf1, cd40 binding protein, cd40bp, lmp1 associated protein, lap1, cap-1. Engineered: yes. 24-residue peptide from lymphotoxin-b receptor. Chain: b.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: traf3 or craf1 or cap1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: the peptide was chemically synthesized, the sequence of the peptide occurs naturally in humans (homo
Biol. unit: Tetramer (from PDB file)
3.50Å     R-factor:   0.266     R-free:   0.315
Authors: C.Li,P.S.Norris,C.Z.Ni,M.L.Havert,E.M.Chiong,B.R.Tran, E.Cabezas,G.Cheng,J.C.Reed,A.C.Satterthwait,C.F.Ware,K.R.El
Key ref:
C.Li et al. (2003). Structurally distinct recognition motifs in lymphotoxin-beta receptor and CD40 for tumor necrosis factor receptor-associated factor (TRAF)-mediated signaling. J Biol Chem, 278, 50523-50529. PubMed id: 14517219 DOI: 10.1074/jbc.M309381200
07-Nov-03     Release date:   06-Jul-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q13114  (TRAF3_HUMAN) -  TNF receptor-associated factor 3
568 a.a.
192 a.a.
Protein chain
Pfam   ArchSchema ?
P36941  (TNR3_HUMAN) -  Tumor necrosis factor receptor superfamily member 3
435 a.a.
24 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of cytokine production   6 terms 


DOI no: 10.1074/jbc.M309381200 J Biol Chem 278:50523-50529 (2003)
PubMed id: 14517219  
Structurally distinct recognition motifs in lymphotoxin-beta receptor and CD40 for tumor necrosis factor receptor-associated factor (TRAF)-mediated signaling.
C.Li, P.S.Norris, C.Z.Ni, M.L.Havert, E.M.Chiong, B.R.Tran, E.Cabezas, J.C.Reed, A.C.Satterthwait, C.F.Ware, K.R.Ely.
Lymphotoxin-beta receptor (LTbetaR) and CD40 are members of the tumor necrosis factor family of signaling receptors that regulate cell survival or death through activation of NF-kappaB. These receptors transmit signals through downstream adaptor proteins called tumor necrosis factor receptor-associated factors (TRAFs). In this study, the crystal structure of a region of the cytoplasmic domain of LTbetaR bound to TRAF3 has revealed an unexpected new recognition motif, 388IPEEGD393, for TRAF3 binding. Although this motif is distinct in sequence and structure from the PVQET motif in CD40 and PIQCT in the regulator TRAF-associated NF-kappaB activator (TANK), recognition is mediated in the same binding crevice on the surface of TRAF3. The results reveal structurally adaptive "hot spots" in the TRAF3-binding crevice that promote molecular interactions driving specific signaling after contact with LTbetaR, CD40, or the downstream regulator TANK.
  Selected figure(s)  
Figure 1.
FIG. 1. Structure of the LT R/TRAF3 complex. Schematic representation of the TRAF3 trimer is shown as a ribbon diagram with each subunit colored separately. The three subunits are stabilized by coiled-coil interactions between the elongated N-terminal helices of each subunit. Each subunit binds one LT R molecule, which is represented as a ball-and-stick model. LT R binds to a crevice at the edge of the TRAF3 -sandwich domain. In this view, the cell membrane is located at the top of the image.
Figure 4.
FIG. 4. LT R/TRAF3 recognition. Close-up view of the molecular contacts between the recognition motif of LT R (ball-and-stick model) bound to the crevice at the edge of TRAF3 (ribbon model) is shown. This set of interactions is identical for each TRAF3 subunit in the trimer. Critical contact residues are labeled, and the labels for TRAF3 residues are underlined. The hydrogen bonds are indicated as dotted lines.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 50523-50529) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20585553 J.Martin (2010).
Beauty is in the eye of the beholder: proteins can recognize binding sites of homologous proteins in more than one way.
  PLoS Comput Biol, 6, e1000821.  
  20516126 L.M.Staudt (2010).
Oncogenic activation of NF-kappaB.
  Cold Spring Harb Perspect Biol, 2, a000109.  
20967291 S.Jaeger, G.Ertaylan, D.van Dijk, U.Leser, and P.Sloot (2010).
Inference of surface membrane factors of HIV-1 infection through functional interaction networks.
  PLoS One, 5, e13139.  
19667091 J.P.Graham, C.R.Moore, and G.A.Bishop (2009).
Roles of the TRAF2/3 binding site in differential B cell signaling by CD40 and its viral oncogenic mimic, LMP1.
  J Immunol, 183, 2966-2973.  
19893624 P.Nakhaei, T.Mesplede, M.Solis, Q.Sun, T.Zhao, L.Yang, T.H.Chuang, C.F.Ware, R.Lin, and J.Hiscott (2009).
The E3 ubiquitin ligase Triad3A negatively regulates the RIG-I/MAVS signaling pathway by targeting TRAF3 for degradation.
  PLoS Pathog, 5, e1000650.  
18613837 C.F.Ware (2008).
Targeting lymphocyte activation through the lymphotoxin and LIGHT pathways.
  Immunol Rev, 223, 186-201.  
17692804 C.M.Annunziata, R.E.Davis, Y.Demchenko, W.Bellamy, A.Gabrea, F.Zhan, G.Lenz, I.Hanamura, G.Wright, W.Xiao, S.Dave, E.M.Hurt, B.Tan, H.Zhao, O.Stephens, M.Santra, D.R.Williams, L.Dang, B.Barlogie, J.D.Shaughnessy, W.M.Kuehl, and L.M.Staudt (2007).
Frequent engagement of the classical and alternative NF-kappaB pathways by diverse genetic abnormalities in multiple myeloma.
  Cancer Cell, 12, 115-130.  
17254331 N.J.Hill, A.Stotland, M.Solomon, P.Secrest, E.Getzoff, and N.Sarvetnick (2007).
Resistance of the target islet tissue to autoimmune destruction contributes to genetic susceptibility in Type 1 diabetes.
  Biol Direct, 2, 5.  
15771586 C.F.Ware (2005).
Network communications: lymphotoxins, LIGHT, and TNF.
  Annu Rev Immunol, 23, 787-819.  
15808506 V.Saridakis, Y.Sheng, F.Sarkari, M.N.Holowaty, K.Shire, T.Nguyen, R.G.Zhang, J.Liao, W.Lee, A.M.Edwards, C.H.Arrowsmith, and L.Frappier (2005).
Structure of the p53 binding domain of HAUSP/USP7 bound to Epstein-Barr nuclear antigen 1 implications for EBV-mediated immortalization.
  Mol Cell, 18, 25-36.
PDB codes: 1yy6 1yze
15743811 Y.S.Kim, S.A.Nedospasov, and Z.G.Liu (2005).
TRAF2 plays a key, nonredundant role in LIGHT-lymphotoxin beta receptor signaling.
  Mol Cell Biol, 25, 2130-2137.  
15546385 K.Schneider, K.G.Potter, and C.F.Ware (2004).
Lymphotoxin and LIGHT signaling pathways and target genes.
  Immunol Rev, 202, 49-66.  
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 codes are shown on the right.