PDBsum entry 1enf

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Toxin PDB id
Protein chain
212 a.a. *
SO4 ×13
Waters ×246
* Residue conservation analysis
PDB id:
Name: Toxin
Title: Crystal structure of staphylococcal enterotoxin h determined resolution
Structure: Enterotoxin h. Chain: a. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
1.69Å     R-factor:   0.164     R-free:   0.187
Authors: M.Hakansson,K.Petersson,H.Nilsson,G.Forsberg,P.Bjork,P.Anton A.Svensson
Key ref:
M.Hâkansson et al. (2000). The crystal structure of staphylococcal enterotoxin H: implications for binding properties to MHC class II and TcR molecules. J Mol Biol, 302, 527-537. PubMed id: 10986116 DOI: 10.1006/jmbi.2000.4093
21-Mar-00     Release date:   19-Apr-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P0A0M0  (ETXH_STAAU) -  Enterotoxin type H
241 a.a.
212 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     pathogenesis   1 term 
  Biochemical function     metal ion binding     1 term  


DOI no: 10.1006/jmbi.2000.4093 J Mol Biol 302:527-537 (2000)
PubMed id: 10986116  
The crystal structure of staphylococcal enterotoxin H: implications for binding properties to MHC class II and TcR molecules.
M.Hâkansson, K.Petersson, H.Nilsson, G.Forsberg, P.Björk, P.Antonsson, L.A.Svensson.
The X-ray structure of the superantigen staphylococcal enterotoxin H (SEH) has been determined at 1.69 A resolution. In this paper we present two structures of zinc-free SEH (apoSEH) and one zinc-loaded form of SEH (ZnSEH). SEH exhibits the conventional superantigen (SAg) fold with two characteristic domains. In ZnSEH one zinc ion per SEH molecule is bound to the C-terminal beta-sheet in the region implicated for major histocompatibility complex class II (MHC class II) binding in SEA, SED and SEE. Surprisingly, the zinc ion has only two ligating amino acid residues His206 and Asp208. The other ligands to the zinc ion are two water molecules. An extensive packing interaction between two symmetry-related molecules in the crystal, 834 A(2)/molecule, forms a cavity that buries the zinc ions of the molecules. This dimer-like interaction is found in two crystal forms. Nevertheless, zinc-dependent dimerisation is not observed in solution, as seen in the case of SED. A unique feature of SEH as compared to other staphylococcal enterotoxins is a large negatively charged surface close to the Zn(2+) site. The interaction of SEH with MHC class II is the strongest known among the staphylococcal enterotoxins. However, SEH seems to lack a SEB-like MHC class II binding site, since the side-chain properties of structurally equivalent amino acid residues in SEH and those in SEB-binding MHC class II differ dramatically. There is also a structural flexibility between the domains of SEH. The domains of two apoSEH structures are related by a 5 degrees rotation leading to at most 3 A difference in C(alpha) positions. Since the T-cell receptor probably interacts with both domains, SEH by this rotation may modulate its binding to different TcR Vbeta-chains.
  Selected figure(s)  
Figure 2.
Figure 2. (a) Dimerisation of MHC class II binding sites. The crystallographic packing of the Zn2+ soaked trigonal form is shown. The zinc ions are represented by yellow spheres and coordinating residues, His206 and Asp208, are drawn as ball and stick. (b) Upper half of identical interaction of SEH molecules in the crystal packing dimer. The hydrogen bonds in the interface are drawn as dotted lines. The second symmetry related molecule is shown in green and indicated with stars. The rings of Pro171 and His206 are packed against Tyr212 and Trp115, respectively. The distances between the rings are 3.3-4.0 Å, typical of hydrophobic interactions. (c) The coordination of the Zn2+ is shown down the 2-fold axis. The zinc ion is coordinated by His206 (2.1 Å), Asp208 Od1 (2.6 Å, hidden in the plane of the 2-fold axis), Asp208 Od2 (1.9 Å) and two water molecules, W1 (2.2 Å) and W2 (2.4 Å). The distance between the zinc ions in symmetry related molecules, is 4.4 Å. The Figures were produced with the MOLSCRIPT program [Kraulis 1991].
Figure 3.
Figure 3. Domain flexibility of SEH. A superposition of the N-terminal domains (residues 23-102) of the trigonal form (green) and the orthorhombic (yellow) form is shown. The corresponding area of SEB interacting with a TcR in the complex structure [Li et al 1998] is marked with a line. The maximum difference between C^a atoms (3 Å) is indicated with an arrow. The drawing was made with the Ribbons program [Carson 1997].
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 302, 527-537) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
19888679 M.Saline, V.Orekhov, K.Lindkvist-Petersson, and B.G.Karlsson (2010).
Backbone resonance assignment of Staphylococcal Enterotoxin H.
  Biomol NMR Assign, 4, 1-4.  
19587800 K.Narayan, E.M.Perkins, G.E.Murphy, S.K.Dalai, M.Edidin, S.Subramaniam, and S.Sadegh-Nasseri (2009).
Staphylococcal enterotoxin A induces small clusters of HLA-DR1 on B cells.
  PLoS One, 4, e6188.  
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.  
17944839 D.Nashev, K.Toshkova, L.Bizeva, O.Akineden, C.Lämmler, and M.Zschöck (2007).
Distribution of enterotoxin genes among carriage- and infection-associated isolates of Staphylococcus aureus.
  Lett Appl Microbiol, 45, 681-685.  
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.  
12676930 M.A.Langlois, Y.El Fakhry, and W.Mourad (2003).
Zinc-binding sites in the N terminus of Mycoplasma arthritidis-derived mitogen permit the dimer formation required for high affinity binding to HLA-DR and for T cell activation.
  J Biol Chem, 278, 22309-22315.  
11811932 D.A.Lawrence, and M.J.McCabe (2002).
Immunomodulation by metals.
  Int Immunopharmacol, 2, 293-302.  
11972634 H.Pettersson, and G.Forsberg (2002).
Staphylococcal enterotoxin H contrasts closely related enterotoxins in species reactivity.
  Immunology, 106, 71-79.  
11934896 Y.I.Chi, I.Sadler, L.M.Jablonski, S.D.Callantine, C.F.Deobald, C.V.Stauffacher, and G.A.Bohach (2002).
Zinc-mediated dimerization and its effect on activity and conformation of staphylococcal enterotoxin type C.
  J Biol Chem, 277, 22839-22846.
PDB code: 1ck1
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
11369867 M.Baker, D.M.Gutman, A.C.Papageorgiou, C.M.Collins, and K.R.Acharya (2001).
Structural features of a zinc binding site in the superantigen strepococcal pyrogenic exotoxin A (SpeA1): implications for MHC class II recognition.
  Protein Sci, 10, 1268-1273.
PDB code: 1ha5
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.