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PDBsum entry 1sbb

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protein Protein-protein interface(s) links
Immune system PDB id
1sbb
Jmol
Contents
Protein chains
238 a.a. *
239 a.a. *
Waters ×159
* Residue conservation analysis
PDB id:
1sbb
Name: Immune system
Title: T-cell receptor beta chain complexed with superantigen seb
Structure: Protein (14.3.D t cell antigen receptor). Chain: a, c. Fragment: beta chain. Engineered: yes. Mutation: yes. Protein (staphylococcal enterotoxin b). Chain: b, d. Synonym: seb. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: mus musculus. Expression_system_taxid: 10090. Staphylococcus aureus. Organism_taxid: 1280. Strain: rn9220. Expressed in: escherichia coli.
Biol. unit: Hetero-Dimer (from PDB file)
Resolution:
2.40Å     R-factor:   0.228     R-free:   0.309
Authors: H.Li,R.A.Mariuzza
Key ref:
H.Li et al. (1998). Three-dimensional structure of the complex between a T cell receptor beta chain and the superantigen staphylococcal enterotoxin B. Immunity, 9, 807-816. PubMed id: 9881971 DOI: 10.1016/S1074-7613(00)80646-9
Date:
22-Feb-99     Release date:   01-Mar-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P01852  (TCB1_MOUSE) -  T-cell receptor beta-1 chain C region
Seq:
Struc:
173 a.a.
238 a.a.*
Protein chains
Pfam   ArchSchema ?
P01552  (ETXB_STAAU) -  Enterotoxin type B
Seq:
Struc:
266 a.a.
239 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     pathogenesis   1 term 

 

 
DOI no: 10.1016/S1074-7613(00)80646-9 Immunity 9:807-816 (1998)
PubMed id: 9881971  
 
 
Three-dimensional structure of the complex between a T cell receptor beta chain and the superantigen staphylococcal enterotoxin B.
H.Li, A.Llera, D.Tsuchiya, L.Leder, X.Ysern, P.M.Schlievert, K.Karjalainen, R.A.Mariuzza.
 
  ABSTRACT  
 
Superantigens (SAGs) are a class of immunostimulatory proteins of bacterial or viral origin that activate T cells by binding to the V beta domain of the T cell antigen receptor (TCR). The three-dimensional structure of the complex between a TCR beta chain (mouse V beta8.2) and the SAG staphylococcal enterotoxin B (SEB) at 2.4 A resolution reveals why SEB recognizes only certain V beta families, as well as why only certain SAGs bind mouse V beta8.2. Models of the TCR-SEB-peptide/MHC class II complex indicate that V alpha interacts with the MHC beta chain in the TCR-SAG-MHC complex. The extent of the interaction is variable and is largely determined by the geometry of V alpha/V beta domain association. This variability can account for the preferential expression of certain V alpha regions among T cells reactive with SEB.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Conformational Differences between Complexed and Uncomplexed Vβ Chain and SEB(A) In the 14.3.d TCR β-SEB structure, uncomplexed Vβ (green) was superposed onto complexed Vβ (red), and uncomplexed SEB (yellow) was superposed onto complexed SEB (blue). Only α-carbon atoms are shown.(B) Closeup of the β-SEB interface. Bound and unbound Vβ and SEB are colored as in (A); Vβ and SEB residues are labeled in black and blue, respectively.
Figure 4.
Figure 4. Comparison of Vβ Structures in the Region of the SEB-Binding Site(A) Mouse Vβ8.2 (yellow) ([3]) superposed onto human Vβ12.3 (blue) ( [23]). The CDR loops are numbered 1, 2, and 3; HV4 is labeled 4. (B) Mouse Vβ8.2 (yellow) superposed onto mouse Vβ2.3 (red) ( [28]). (C) Mouse Vβ8.2 (yellow) superposed onto mouse Vβ5.2 (green) ( [64]). The SEB-binding site of mouse Vβ8.2 is circled in each panel.
 
  The above figures are reprinted by permission from Cell Press: Immunity (1998, 9, 807-816) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20070903 K.S.Seo, J.Y.Park, D.S.Terman, and G.A.Bohach (2010).
A quantitative real time PCR method to analyze T cell receptor Vbeta subgroup expansion by staphylococcal superantigens.
  J Transl Med, 8, 2.  
21081917 M.Saline, K.E.Rödström, G.Fischer, V.Y.Orekhov, B.G.Karlsson, and K.Lindkvist-Petersson (2010).
The structure of superantigen complexed with TCR and MHC reveals novel insights into superantigenic T cell activation.
  Nat Commun, 1, 119.
PDB codes: 2xn9 2xna
20109735 P.M.Schlievert, K.L.Strandberg, Y.C.Lin, M.L.Peterson, and D.Y.Leung (2010).
Secreted virulence factor comparison between methicillin-resistant and methicillin-sensitive Staphylococcus aureus, and its relevance to atopic dermatitis.
  J Allergy Clin Immunol, 125, 39-49.  
20554806 T.K.Inskeep, C.Stahl, J.Odle, J.Oakes, L.Hudson, K.L.Bost, and K.J.Piller (2010).
Oral vaccine formulations stimulate mucosal and systemic antibody responses against staphylococcal enterotoxin B in a piglet model.
  Clin Vaccine Immunol, 17, 1163-1169.  
19609675 Z.Lin, D.P.Kotler, P.M.Schlievert, and E.M.Sordillo (2010).
Staphylococcal enterocolitis: forgotten but not gone?
  Dig Dis Sci, 55, 1200-1207.  
18716897 Y.Ou, C.Tong, Y.Zhang, P.Cai, J.Gu, Y.Liu, H.Liu, H.Wang, B.Chu, and P.Zhu (2009).
An improved design of PCR primers for detection of human T cell receptor beta chain repertoire.
  Mol Biol Rep, 36, 145-152.  
18194268 D.J.Miles, M.Sanneh, B.Holder, S.Crozier, S.Nyamweya, E.S.Touray, M.S.Palmero, S.M.Zaman, S.Rowland-Jones, M.van der Sande, and H.Whittle (2008).
Cytomegalovirus infection induces T-cell differentiation without impairing antigen-specific responses in Gambian infants.
  Immunology, 124, 388-400.  
17268555 B.Moza, A.K.Varma, R.A.Buonpane, P.Zhu, C.A.Herfst, M.J.Nicholson, A.K.Wilbuer, N.P.Seth, K.W.Wucherpfennig, J.K.McCormick, D.M.Kranz, and E.J.Sundberg (2007).
Structural basis of T-cell specificity and activation by the bacterial superantigen TSST-1.
  EMBO J, 26, 1187-1197.
PDB code: 2ij0
17560120 E.J.Sundberg, L.Deng, and R.A.Mariuzza (2007).
TCR recognition of peptide/MHC class II complexes and superantigens.
  Semin Immunol, 19, 262-271.  
17427250 M.M.Fernández, S.Bhattacharya, M.C.De Marzi, P.H.Brown, M.Kerzic, P.Schuck, R.A.Mariuzza, and E.L.Malchiodi (2007).
Superantigen natural affinity maturation revealed by the crystal structure of staphylococcal enterotoxin G and its binding to T-cell receptor Vbeta8.2.
  Proteins, 68, 389-402.  
17560605 S.Günther, A.K.Varma, B.Moza, K.J.Kasper, A.W.Wyatt, P.Zhu, A.K.Rahman, Y.Li, R.A.Mariuzza, J.K.McCormick, and E.J.Sundberg (2007).
A novel loop domain in superantigens extends their T cell receptor recognition site.
  J Mol Biol, 371, 210-221.
PDB codes: 2nts 2ntt
17045255 G.Muralimohan, and A.T.Vella (2006).
A role for IFNgamma in differential superantigen stimulation of conventional versus plasmacytoid DCs.
  Cell Immunol, 242, 9.  
16829512 M.M.Fernández, R.Guan, C.P.Swaminathan, E.L.Malchiodi, and R.A.Mariuzza (2006).
Crystal structure of staphylococcal enterotoxin I (SEI) in complex with a human major histocompatibility complex class II molecule.
  J Biol Chem, 281, 25356-25364.
PDB code: 2g9h
16260763 H.Li, S.Van Vranken, Y.Zhao, Z.Li, Y.Guo, L.Eisele, and Y.Li (2005).
Crystal structures of T cell receptor (beta) chains related to rheumatoid arthritis.
  Protein Sci, 14, 3025-3038.
PDB codes: 2axh 2axj
15702314 M.F.Desimone, M.C.De Marzi, G.J.Copello, M.M.Fernández, E.L.Malchiodi, and L.E.Diaz (2005).
Efficient preservation in a silicon oxide matrix of Escherichia coli, producer of recombinant proteins.
  Appl Microbiol Biotechnol, 68, 747-752.  
15784559 M.L.Peterson, K.Ault, M.J.Kremer, A.J.Klingelhutz, C.C.Davis, C.A.Squier, and P.M.Schlievert (2005).
The innate immune system is activated by stimulation of vaginal epithelial cells with Staphylococcus aureus and toxic shock syndrome toxin 1.
  Infect Immun, 73, 2164-2174.  
15935880 N.J.Mantis (2005).
Vaccines against the category B toxins: Staphylococcal enterotoxin B, epsilon toxin and ricin.
  Adv Drug Deliv Rev, 57, 1424-1439.  
14604991 E.Hong-Geller, M.Möllhoff, P.R.Shiflett, and G.Gupta (2004).
Design of chimeric receptor mimics with different TcRVbeta isoforms. Type-specific inhibition of superantigen pathogenesis.
  J Biol Chem, 279, 5676-5684.  
15049778 K.Petersson, G.Forsberg, and B.Walse (2004).
Interplay between superantigens and immunoreceptors.
  Scand J Immunol, 59, 345-355.  
15479236 M.C.De Marzí, M.M.Fernández, E.J.Sundberg, L.Molinero, N.W.Zwirner, A.S.Llera, R.A.Mariuzza, and E.L.Malchiodi (2004).
Cloning, expression and interaction of human T-cell receptors with the bacterial superantigen SSA.
  Eur J Biochem, 271, 4075-4083.  
12794937 B.M.Paddle (2003).
Therapy and prophylaxis of inhaled biological toxins.
  J Appl Toxicol, 23, 139-170.  
12784373 C.J.Camacho, and D.W.Gatchell (2003).
Successful discrimination of protein interactions.
  Proteins, 52, 92-97.  
12962633 E.J.Sundberg, P.S.Andersen, P.M.Schlievert, K.Karjalainen, and R.A.Mariuzza (2003).
Structural, energetic, and functional analysis of a protein-protein interface at distinct stages of affinity maturation.
  Structure, 11, 1151-1161.
PDB codes: 1jwm 1jws 1jwu
12784377 J.J.Gray, S.E.Moughon, T.Kortemme, O.Schueler-Furman, K.M.Misura, A.V.Morozov, and D.Baker (2003).
Protein-protein docking predictions for the CAPRI experiment.
  Proteins, 52, 118-122.  
12784369 R.Chen, W.Tong, J.Mintseris, L.Li, and Z.Weng (2003).
ZDOCK predictions for the CAPRI challenge.
  Proteins, 52, 68-73.  
12802924 S.D'Costa, and J.L.Hurwitz (2003).
Customized mitogen or antibody treatments enhance the sensitivity of lymphoid tumors to 5-fluorouracil in vitro and in vivo.
  Leuk Lymphoma, 44, 841-847.  
14579365 Z.Wang, and J.Moult (2003).
Three-dimensional structural location and molecular functional effects of missense SNPs in the T cell receptor Vbeta domain.
  Proteins, 53, 748-757.  
11790531 E.J.Sundberg, Y.Li, and R.A.Mariuzza (2002).
So many ways of getting in the way: diversity in the molecular architecture of superantigen-dependent T-cell signaling complexes.
  Curr Opin Immunol, 14, 36-44.  
11847286 H.I.Krupka, B.W.Segelke, R.G.Ulrich, S.Ringhofer, M.Knapp, and B.Rupp (2002).
Structural basis for abrogated binding between staphylococcal enterotoxin A superantigen vaccine and MHC-IIalpha.
  Protein Sci, 11, 642-651.
PDB code: 1dyq
11972634 H.Pettersson, and G.Forsberg (2002).
Staphylococcal enterotoxin H contrasts closely related enterotoxins in species reactivity.
  Immunology, 106, 71-79.  
11290341 C.T.Morita, H.Li, J.G.Lamphear, R.R.Rich, J.D.Fraser, R.A.Mariuzza, and H.K.Lee (2001).
Superantigen recognition by gammadelta T cells: SEA recognition site for human Vgamma2 T cell receptors.
  Immunity, 14, 331-344.  
11544350 J.K.McCormick, J.M.Yarwood, and P.M.Schlievert (2001).
Toxic shock syndrome and bacterial superantigens: an update.
  Annu Rev Microbiol, 55, 77.  
11432818 K.Petersson, M.Håkansson, H.Nilsson, G.Forsberg, L.A.Svensson, A.Liljas, and B.Walse (2001).
Crystal structure of a superantigen bound to MHC class II displays zinc and peptide dependence.
  EMBO J, 20, 3306-3312.
PDB code: 1hxy
11119525 P.M.Orwin, D.Y.Leung, H.L.Donahue, R.P.Novick, and P.M.Schlievert (2001).
Biochemical and biological properties of Staphylococcal enterotoxin K.
  Infect Immun, 69, 360-366.  
11576216 P.S.Evans, P.J.Enders, C.Yin, T.J.Ruckwardt, M.Malkovsky, and C.D.Pauza (2001).
In vitro stimulation with a non-peptidic alkylphosphate expands cells expressing Vgamma2-Jgamma1.2/Vdelta2 T-cell receptors.
  Immunology, 104, 19-27.  
  11890612 S.Casares, C.A.Bona, and T.D.Brumeanu (2001).
Modulation of CD4 T cell function by soluble MHC II-peptide chimeras.
  Int Rev Immunol, 20, 547-573.  
10920396 A.C.Papageorgiou, and K.R.Acharya (2000).
Microbial superantigens: from structure to function.
  Trends Microbiol, 8, 369-375.  
10704464 H.R.Churchill, P.S.Andersen, E.A.Parke, R.A.Mariuzza, and D.M.Kranz (2000).
Mapping the energy of superantigen Staphylococcus enterotoxin C3 recognition of an alpha/beta T cell receptor using alanine scanning mutagenesis.
  J Exp Med, 191, 835-846.  
10651924 J.D.Hayball, and R.A.Lake (2000).
Partial T cell activation with an altered superantigenic ligand.
  Immunol Cell Biol, 78, 13-19.  
10816471 L.T.Pang, W.W.Kum, and A.W.Chow (2000).
Inhibition of staphylococcal enterotoxin B-induced lymphocyte proliferation and tumor necrosis factor alpha secretion by MAb5, an anti-toxic shock syndrome toxin 1 monoclonal antibody.
  Infect Immun, 68, 3261-3268.  
10805799 M.Graille, E.A.Stura, A.L.Corper, B.J.Sutton, M.J.Taussig, J.B.Charbonnier, and G.J.Silverman (2000).
Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: structural basis for recognition of B-cell receptors and superantigen activity.
  Proc Natl Acad Sci U S A, 97, 5399-5404.
PDB code: 1dee
10627489 M.M.Dinges, P.M.Orwin, and P.M.Schlievert (2000).
Exotoxins of Staphylococcus aureus.
  Clin Microbiol Rev, 13, 16.  
10948118 M.Roggiani, J.A.Stoehr, S.B.Olmsted, Y.V.Matsuka, S.Pillai, D.H.Ohlendorf, and P.M.Schlievert (2000).
Toxoids of streptococcal pyrogenic exotoxin A are protective in rabbit models of streptococcal toxic shock syndrome.
  Infect Immun, 68, 5011-5017.  
10617783 R.G.Ulrich (2000).
Evolving superantigens of Staphylococcus aureus.
  FEMS Immunol Med Microbiol, 27, 1-7.  
10229190 P.S.Andersen, P.M.Lavoie, R.P.Sékaly, H.Churchill, D.M.Kranz, P.M.Schlievert, K.Karjalainen, and R.A.Mariuzza (1999).
Role of the T cell receptor alpha chain in stabilizing TCR-superantigen-MHC class II complexes.
  Immunity, 10, 473-483.  
  10569782 Z.Yan, D.C.Yang, R.Neill, and M.Jett (1999).
Production of tumor necrosis factor alpha in human T lymphocytes by staphylococcal enterotoxin B correlates with toxin-induced proliferation and is regulated through protein kinase C.
  Infect Immun, 67, 6611-6618.  
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.