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PDBsum entry 3seb
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References listed in PDB file
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Key reference
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Title
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Crystal structure of microbial superantigen staphylococcal enterotoxin b at 1.5 a resolution: implications for superantigen recognition by mhc class ii molecules and t-Cell receptors.
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Authors
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A.C.Papageorgiou,
H.S.Tranter,
K.R.Acharya.
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Ref.
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J Mol Biol, 1998,
277,
61-79.
[DOI no: ]
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PubMed id
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Abstract
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Staphylococcal enterotoxin B is a member of a family of toxins known as
superantigens that activate a large number of T-cells (up to 20%) by
cross-linking MHC class II molecules with T-cell receptors in a Vbeta-restricted
fashion. The crystal structure of staphylococcal enterotoxin B presented here
has been determined at 1.5 A resolution, the highest resolution so far for a
superantigen. The final model contains 1948 protein atoms and 177 water
molecules and has excellent geometry with root-mean-square (rms) deviation of
0.007 A and 1.73 degrees in bond lengths and bond angles, respectively. The
overall fold is similar to that of other microbial superantigens, but as it
lacks the zinc-binding site found in other members of this family, such as
staphylococcal enterotoxin A, C2 and D, this enterotoxin possesses only one MHC
class II binding site. Comparison of the crystal structure of free SEB and in
complex with an MHC class II molecule revealed no major changes in the
MHC-binding site upon complex formation. However, a number of water molecules
found in the free SEB may be displaced in the complex or contribute further to
its stability. Detailed analysis of the TcR-binding site of SEB, SEA and SEC2
shows significant differences which may account for the ability of each
superantigen to bind specific Vbeta sequences.
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Figure 6.
Figure 6. Stereo views displaying (a) a C^α-trace of SEB
(every tenth residue is numbered); and (b) a comparison of
C^α-traces of SEB (black), SEC2 (green), SEA (blue) and TSST-1
(orange).
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Figure 9.
Figure 9. Histogram of the B-factor distribution for the
water molecules in SEB.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
277,
61-79)
copyright 1998.
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Secondary reference #1
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Title
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Superantigens as immunomodulators: recent structural insights.
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Authors
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A.C.Papageorgiou,
K.R.Acharya.
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Ref.
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Structure, 1997,
5,
991-996.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. Ribbon diagrams of the structures of two
superantigen-DR1 complexes: (a) SEB-DR1 [16] and (b) TSST-1-DR1
[17]. The peptide antigen is coloured in yellow; a helices are
in red and b sheets in green.
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The above figure is
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #2
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Title
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Crystal structure of the superantigen enterotoxin c2 from staphylococcus aureus reveals a zinc-Binding site.
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Authors
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A.C.Papageorgiou,
K.R.Acharya,
R.Shapiro,
E.F.Passalacqua,
R.D.Brehm,
H.S.Tranter.
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Ref.
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Structure, 1995,
3,
769-779.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2. Stereoviews displaying (a) a Cα trace for SEC2 and
(b) a comparison of Cα traces for SEC2 (black), SEB (red) and
TSST-1 (green). The rms deviation between the Cα positions of
206 equivalent residues in SEC2 and SEB crystal structures is
0.94 å and the corresponding deviation between the Cα
positions of 181 equivalent residues in SEC2 and TSST-1 crystal
structures is 2.95 å. Structural alignments were performed
using the Structure Homology Program (SHP) [64]. Figure 2.
Stereoviews displaying (a) a Cα trace for SEC2 and (b) a
comparison of Cα traces for SEC2 (black), SEB (red) and TSST-1
(green). The rms deviation between the Cα positions of 206
equivalent residues in SEC2 and SEB crystal structures is 0.94
å and the corresponding deviation between the Cα
positions of 181 equivalent residues in SEC2 and TSST-1 crystal
structures is 2.95 å. Structural alignments were performed
using the Structure Homology Program (SHP) [[4]64].
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Figure 6.
Figure 6. Representative portion of the 2|F[o]|–|F[c]|
electron-density map of SEC2 contoured at 1.0 σ using the
refined structure at 2.0 å resolution. Figure 6.
Representative portion of the 2|F[o]|–|F[c]| electron-density
map of SEC2 contoured at 1.0 σ using the refined structure at
2.0 å resolution.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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