PDBsum entry 1m4v

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Immune system PDB id
Protein chains
196 a.a. *
Waters ×377
* Residue conservation analysis
PDB id:
Name: Immune system
Title: Crystal structure of set3, a superantigen-like protein from staphylococcus aureus
Structure: Set3, superantigen-like protein. Chain: a, b. Synonym: exotoxin-like protein. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Gene: set3. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
1.90Å     R-factor:   0.205     R-free:   0.240
Authors: V.L.Arcus,R.Langley,T.Proft,J.D.Fraser,E.N.Baker
Key ref:
V.L.Arcus et al. (2002). The Three-dimensional structure of a superantigen-like protein, SET3, from a pathogenicity island of the Staphylococcus aureus genome. J Biol Chem, 277, 32274-32281. PubMed id: 12082105 DOI: 10.1074/jbc.M203914200
05-Jul-02     Release date:   17-Jul-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9ZFS6  (Q9ZFS6_STAAU) -  Exotoxin 3
234 a.a.
196 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 20 residue positions (black crosses)

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


DOI no: 10.1074/jbc.M203914200 J Biol Chem 277:32274-32281 (2002)
PubMed id: 12082105  
The Three-dimensional structure of a superantigen-like protein, SET3, from a pathogenicity island of the Staphylococcus aureus genome.
V.L.Arcus, R.Langley, T.Proft, J.D.Fraser, E.N.Baker.
The staphylococcal enterotoxin-like toxins (SETs) are a family of proteins encoded within the Staphylococcus aureus genome that were identified by their similarity to the well described bacterial superantigens. The first crystal structure of a member of the SET family, SET3, has been determined to 1.9 A (R = 0.205, R(free) = 0.240) and reveals a fold characteristic of the superantigen family but with significant differences. The SET proteins are secreted at varying levels by staphylococcal isolates, and seroconversion studies of normal individuals indicate that they are strongly antigenic to humans. Recombinant SETs do not exhibit any of the properties expected of superantigens such as major histocompatibility complex class II binding or broad T-cell activation, suggesting they have an entirely different function. The fact that the whole gene family is clustered within the pathogenicity island SaIn2 of the S. aureus genome suggests that they are involved in host/pathogen interactions.
  Selected figure(s)  
Figure 2.
Fig. 2. SET3 structure. Top, stereo view of the C backbone trace of SET3 colored from the N terminus to the C terminus (blue to red). Selected residues are labeled according to their single-letter amino acid code and their number in the sequence. A loop spanning five residues (83-86) is not visible in the electron density for the SET3 structure and is omitted in this figure. Lower left, schematic ribbon diagram of SET3 showing the canonical superantigen fold viewed along the pseudo 2-fold axis of the putative dimer. The N and C termini are labeled; the N-terminal OB-fold domain is at the top left and bottom right of the structure. This panel was drawn using PyMol ( Lower right, the electrostatic potential at the protein surface looking down the pseudo crystallographic 2-fold axis showing the concentrations of positive charge at each end of the individual monomers. This panel was drawn using GRASP (26).
Figure 3.
Fig. 3. Structural comparison of the N-terminal "binding face." A structural alignment of the N-terminal binding faces of SET3, TSST, and SPE-C. TSST is shown in gray, and residues that interact with MHC-II in the TSST·MHC-II complex are identified by small black spheres and labeled using the single-letter amino acid codes. Residues in SET3 and SPE-C at equivalent positions are shown in the sequence alignment at the bottom of the figure. The C trace for SET3 is shown in red and for SPE-C is shown in blue.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 32274-32281) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20545943 J.Bestebroer, P.C.Aerts, S.H.Rooijakkers, M.K.Pandey, J.Köhl, J.A.van Strijp, and Haas (2010).
Functional basis for complement evasion by staphylococcal superantigen-like 7.
  Cell Microbiol, 12, 1506-1516.  
20479083 S.Itoh, E.Hamada, G.Kamoshida, K.Takeshita, T.Oku, and T.Tsuji (2010).
Staphylococcal superantigen-like protein 5 inhibits matrix metalloproteinase 9 from human neutrophils.
  Infect Immun, 78, 3298-3305.  
18941109 J.Bestebroer, K.P.van Kessel, H.Azouagh, A.M.Walenkamp, I.G.Boer, R.A.Romijn, J.A.van Strijp, and Haas (2009).
Staphylococcal SSL5 inhibits leukocyte activation by chemokines and anaphylatoxins.
  Blood, 113, 328-337.  
18710864 H.K.Ono, K.Omoe, K.Imanishi, Y.Iwakabe, D.L.Hu, H.Kato, N.Saito, A.Nakane, T.Uchiyama, and K.Shinagawa (2008).
Identification and characterization of two novel staphylococcal enterotoxins, types S and T.
  Infect Immun, 76, 4999-5005.  
18039711 A.Zemla, B.Geisbrecht, J.Smith, M.Lam, B.Kirkpatrick, M.Wagner, T.Slezak, and C.E.Zhou (2007).
STRALCP--structure alignment-based clustering of proteins.
  Nucleic Acids Res, 35, e150.  
17848512 P.A.Ramsland, N.Willoughby, H.M.Trist, W.Farrugia, P.M.Hogarth, J.D.Fraser, and B.D.Wines (2007).
Structural basis for evasion of IgA immunity by Staphylococcus aureus revealed in the complex of SSL7 with Fc of human IgA1.
  Proc Natl Acad Sci U S A, 104, 15051-15056.
PDB code: 2qej
17681885 T.Chavakis, K.T.Preissner, and M.Herrmann (2007).
The anti-inflammatory activities of Staphylococcus aureus.
  Trends Immunol, 28, 408-418.  
15213171 A.M.Al-Shangiti, C.E.Naylor, S.P.Nair, D.C.Briggs, B.Henderson, and B.M.Chain (2004).
Structural relationships and cellular tropism of staphylococcal superantigen-like proteins.
  Infect Immun, 72, 4261-4270.
PDB codes: 1v1o 1v1p
15213151 S.Holtfreter, K.Bauer, D.Thomas, C.Feig, V.Lorenz, K.Roschack, E.Friebe, K.Selleng, S.Lövenich, T.Greve, A.Greinacher, B.Panzig, S.Engelmann, G.Lina, and B.M.Bröker (2004).
egc-Encoded superantigens from Staphylococcus aureus are neutralized by human sera much less efficiently than are classical staphylococcal enterotoxins or toxic shock syndrome toxin.
  Infect Immun, 72, 4061-4071.  
12704157 J.R.Fitzgerald, S.D.Reid, E.Ruotsalainen, T.J.Tripp, M.Liu, R.Cole, P.Kuusela, P.M.Schlievert, A.Järvinen, and J.M.Musser (2003).
Genome diversification in Staphylococcus aureus: Molecular evolution of a highly variable chromosomal region encoding the Staphylococcal exotoxin-like family of proteins.
  Infect Immun, 71, 2827-2838.  
14500536 K.Omoe, D.L.Hu, H.Takahashi-Omoe, A.Nakane, and K.Shinagawa (2003).
Identification and characterization of a new staphylococcal enterotoxin-related putative toxin encoded by two kinds of plasmids.
  Infect Immun, 71, 6088-6094.  
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.