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Color Plates

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Figures

Image of Color Plate 1 (Chapter 2). Cartoon model of TSST-1, showing eukaryotic cell binding domains. Purple residue (Q136) is involved in Vβ2-TCR binding; Red residues (G31/S32) are involved in α-chain MHC II binding; and orange residues (dodecapeptide) are hypothesized to be involved in epithelial cell binding. Residues 120 to 123 in the dodecapeptide region are dominant surface-exposed residues.

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Color Plate 1 (Chapter 2). Cartoon model of TSST-1, showing eukaryotic cell binding domains. Purple residue (Q136) is involved in Vβ2-TCR binding; Red residues (G31/S32) are involved in α-chain MHC II binding; and orange residues (dodecapeptide) are hypothesized to be involved in epithelial cell binding. Residues 120 to 123 in the dodecapeptide region are dominant surface-exposed residues.

Cartoon model of TSST-1, showing eukaryotic cell binding domains. Purple residue (Q136) is involved in Vβ2-TCR binding; Red residues (G31/S32) are involved in α-chain MHC II binding; and orange residues (dodecapeptide) are hypothesized to be involved in epithelial cell binding. Residues 120 to 123 in the dodecapeptide region are dominant surface-exposed residues.

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 2 (Chapter 5). Tertiary structure of SEA, YPMa, the capsid protein of STNV, and ACRP. Structural data for SEA (accession number 1SXT), YPMa (accession number 1PM4), ACRP (accession number 1C28), and STNV (accession number 2STV) are depicted by Cn3D. α-Helices and β-sheets are presented as cylinders and arrows, respectively.

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Color Plate 2 (Chapter 5). Tertiary structure of SEA, YPMa, the capsid protein of STNV, and ACRP. Structural data for SEA (accession number 1SXT), YPMa (accession number 1PM4), ACRP (accession number 1C28), and STNV (accession number 2STV) are depicted by Cn3D. α-Helices and β-sheets are presented as cylinders and arrows, respectively.

Tertiary structure of SEA, YPMa, the capsid protein of STNV, and ACRP. Structural data for SEA (accession number 1SXT), YPMa (accession number 1PM4), ACRP (accession number 1C28), and STNV (accession number 2STV) are depicted by Cn3D. α-Helices and β-sheets are presented as cylinders and arrows, respectively.

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 3 (Chapter 6). The structure of SMEZ-2. (A) Ribbon diagram showing the arrangement of secondary structure elements for SMEZ-2 (α-helices are red, β-sheets are green, and loops are grey) (6). The two domains and the N-terminal helix are labeled. A bound Zn2+ ion is shown as a blue sphere along with the three residues that ligate this ion (H162, H202, D204). This ion is a key contributor to the interaction between SMEZ-2 and MHC-II. (B) An “HMM Logo” representation (39) of the superantigen signature sequence showing the amino acid conservation in the region of the central α-helix. Numbers beneath the figure are those for SMEZ-2. (C) The position of the conserved residues in the structure of SMEZ-2 and their hydrogen-bonding patterns. Note that this figure is rotated 180° in the vertical axis in comparison to (A). (D) Allelic variation at the surface of SMEZ-2 is shown in blue. The molecules are rotated 180° in the vertical axis with respect to each other. This figure along with subsequent figures were drawn using the molecular graphics program PyMol (DeLano Scientific, http://www.pymol.org).

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Color Plate 3 (Chapter 6). The structure of SMEZ-2. (A) Ribbon diagram showing the arrangement of secondary structure elements for SMEZ-2 (α-helices are red, β-sheets are green, and loops are grey) (6). The two domains and the N-terminal helix are labeled. A bound Zn2+ ion is shown as a blue sphere along with the three residues that ligate this ion (H162, H202, D204). This ion is a key contributor to the interaction between SMEZ-2 and MHC-II. (B) An “HMM Logo” representation (39) of the superantigen signature sequence showing the amino acid conservation in the region of the central α-helix. Numbers beneath the figure are those for SMEZ-2. (C) The position of the conserved residues in the structure of SMEZ-2 and their hydrogen-bonding patterns. Note that this figure is rotated 180° in the vertical axis in comparison to (A). (D) Allelic variation at the surface of SMEZ-2 is shown in blue. The molecules are rotated 180° in the vertical axis with respect to each other. This figure along with subsequent figures were drawn using the molecular graphics program PyMol (DeLano Scientific, http://www.pymol.org).

The structure of SMEZ-2. (A) Ribbon diagram showing the arrangement of secondary structure elements for SMEZ-2 (α-helices are red, β-sheets are green, and loops are grey) (6). The two domains and the N-terminal helix are labeled. A bound Zn ion is shown as a blue sphere along with the three residues that ligate this ion (H162, H202, D204). This ion is a key contributor to the interaction between SMEZ-2 and MHC-II. (B) An “HMM Logo” representation (39) of the superantigen signature sequence showing the amino acid conservation in the region of the central α-helix. Numbers beneath the figure are those for SMEZ-2. (C) The position of the conserved residues in the structure of SMEZ-2 and their hydrogen-bonding patterns. Note that this figure is rotated 180° in the vertical axis in comparison to (A). (D) Allelic variation at the surface of SMEZ-2 is shown in blue. The molecules are rotated 180° in the vertical axis with respect to each other. This figure along with subsequent figures were drawn using the molecular graphics program PyMol (DeLano Scientific, http://www.pymol.org).

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 4 (Chapter 6). Superantigen binding to MHC-II. (A) SEB is shown binding to the α-chain of MHC-II. At left, the complex is shown as a surface with SEB in blue and MHC-II in red. The surface is semitransparent and the protein chains are shown as Cα traces beneath the surface. Details of the interacting residues are shown at the right of the figure. Residues at the interface from SEB are shown in blue and residues from MHC-II are orange. The principal α-chain helix for MHC-II is red and the bound peptide is black. The coordinates used to draw this figure have PDB code 1SEB (17). (B) SPE-C is shown binding to the β-chain of MHC-II. At right, the complex is shown as a surface with SPE-C in blue and MHC-II in red. The surface is semitransparent and the protein chains are shown as Cα traces. Details of the interacting residues are shown at the left of the figure. Residues at the interface from SPE-C are shown in blue and single Zn2+-ligating histidine from MHC-II is orange. The Zn2+ ion at the protein-protein interface is shown as a light-blue sphere. The peptide bound to MHC-II is black. The coordinates used to draw this figure have PDB code 1HQR (24).

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Color Plate 4 (Chapter 6). Superantigen binding to MHC-II. (A) SEB is shown binding to the α-chain of MHC-II. At left, the complex is shown as a surface with SEB in blue and MHC-II in red. The surface is semitransparent and the protein chains are shown as Cα traces beneath the surface. Details of the interacting residues are shown at the right of the figure. Residues at the interface from SEB are shown in blue and residues from MHC-II are orange. The principal α-chain helix for MHC-II is red and the bound peptide is black. The coordinates used to draw this figure have PDB code 1SEB (17). (B) SPE-C is shown binding to the β-chain of MHC-II. At right, the complex is shown as a surface with SPE-C in blue and MHC-II in red. The surface is semitransparent and the protein chains are shown as Cα traces. Details of the interacting residues are shown at the left of the figure. Residues at the interface from SPE-C are shown in blue and single Zn2+-ligating histidine from MHC-II is orange. The Zn2+ ion at the protein-protein interface is shown as a light-blue sphere. The peptide bound to MHC-II is black. The coordinates used to draw this figure have PDB code 1HQR (24).

Superantigen binding to MHC-II. (A) SEB is shown binding to the α-chain of MHC-II. At left, the complex is shown as a surface with SEB in blue and MHC-II in red. The surface is semitransparent and the protein chains are shown as Cα traces beneath the surface. Details of the interacting residues are shown at the right of the figure. Residues at the interface from SEB are shown in blue and residues from MHC-II are orange. The principal α-chain helix for MHC-II is red and the bound peptide is black. The coordinates used to draw this figure have PDB code 1SEB (17). (B) SPE-C is shown binding to the β-chain of MHC-II. At right, the complex is shown as a surface with SPE-C in blue and MHC-II in red. The surface is semitransparent and the protein chains are shown as Cα traces. Details of the interacting residues are shown at the left of the figure. Residues at the interface from SPE-C are shown in blue and single Zn-ligating histidine from MHC-II is orange. The Zn ion at the protein-protein interface is shown as a light-blue sphere. The peptide bound to MHC-II is black. The coordinates used to draw this figure have PDB code 1HQR (24).

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 5 (Chapter 6). The SAg/TCR β-chain complexes. (A) The structure of SEB bound to the β-chain of the TCR (22). At left the TCR and SEB proteins are shown as ribbon diagrams and regions of the proteins that lie at the interface are shown as sticks. At right this region is expanded and the three hydrogen bonds at the interface are shown as gold broken lines. Residues from SEB are shown as blue sticks and residues from the TCR are shown as grey sticks. Some residues and loops are labeled for reference. (B) The structure of SPE-C bound to the TCR β-chain (41). As in (A), at left is a ribbon diagram of the complex with the two proteins labeled and at right is an expanded region showing the interacting side chains and loops. The nine hydrogen bonds are shown although some are obscured.

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Color Plate 5 (Chapter 6). The SAg/TCR β-chain complexes. (A) The structure of SEB bound to the β-chain of the TCR (22). At left the TCR and SEB proteins are shown as ribbon diagrams and regions of the proteins that lie at the interface are shown as sticks. At right this region is expanded and the three hydrogen bonds at the interface are shown as gold broken lines. Residues from SEB are shown as blue sticks and residues from the TCR are shown as grey sticks. Some residues and loops are labeled for reference. (B) The structure of SPE-C bound to the TCR β-chain (41). As in (A), at left is a ribbon diagram of the complex with the two proteins labeled and at right is an expanded region showing the interacting side chains and loops. The nine hydrogen bonds are shown although some are obscured.

The SAg/TCR β-chain complexes. (A) The structure of SEB bound to the β-chain of the TCR (22). At left the TCR and SEB proteins are shown as ribbon diagrams and regions of the proteins that lie at the interface are shown as sticks. At right this region is expanded and the three hydrogen bonds at the interface are shown as gold broken lines. Residues from SEB are shown as blue sticks and residues from the TCR are shown as grey sticks. Some residues and loops are labeled for reference. (B) The structure of SPE-C bound to the TCR β-chain (41). As in (A), at left is a ribbon diagram of the complex with the two proteins labeled and at right is an expanded region showing the interacting side chains and loops. The nine hydrogen bonds are shown although some are obscured.

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 6 (Chapter 6). The putative MHC-II/SEB/TCR complex. A hypothesized functional complex of SEB, MHC-II, and TCR. This complex is modeled based on the binary complexes of SEB/MHC-II (PDB code 1SEB [17]), SPE-A/TCRβ (PDB code 1L0Y [41]), and TCRαβ (PDB code 1J8H [15]). The α-chain of MHC-II is shown in green and the β-chain is shown in blue. The bound peptide is red. SEB is orange and the TCR β-chain is yellow. The TCR β-chain is brown.

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Color Plate 6 (Chapter 6). The putative MHC-II/SEB/TCR complex. A hypothesized functional complex of SEB, MHC-II, and TCR. This complex is modeled based on the binary complexes of SEB/MHC-II (PDB code 1SEB [17]), SPE-A/TCRβ (PDB code 1L0Y [41]), and TCRαβ (PDB code 1J8H [15]). The α-chain of MHC-II is shown in green and the β-chain is shown in blue. The bound peptide is red. SEB is orange and the TCR β-chain is yellow. The TCR β-chain is brown.

The putative MHC-II/SEB/TCR complex. A hypothesized functional complex of SEB, MHC-II, and TCR. This complex is modeled based on the binary complexes of SEB/MHC-II (PDB code 1SEB [17]), SPE-A/TCRβ (PDB code 1L0Y [41]), and TCRαβ (PDB code 1J8H [15]). The α-chain of MHC-II is shown in green and the β-chain is shown in blue. The bound peptide is red. SEB is orange and the TCR β-chain is yellow. The TCR β-chain is brown.

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 7 (Chapter 6). The putative MHC-II/SPE-C/TCR complex and MHC-II cross-linking by SPE-C dimerization. (A) A hypothesized functional complex of SPE-C, MHC-II, and TCR. This model has been built based on the binary complexes of SPE-C/MHC-II (PDB code 1HQR [24]), SPE-C/TCRβ (PDB code 1KTK [41]) and TCRαβ (PDB code 1J8H [15]). Colors are the same as for Color Plate 5 except that SPE-C is colored raspberry and the zinc ion at the SPE-C/MHC-II interface is shown as a light-blue sphere. (B) A possible mode for cross-linking MHC-II at the surface of APCs via SPE-C dimerization. This model has been built using the SPE-C/MHC-II complex along with the SPE-C dimer seen in the crystal structure of SPE-C alone (PDB code 1AN8 [38]).

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Color Plate 7 (Chapter 6). The putative MHC-II/SPE-C/TCR complex and MHC-II cross-linking by SPE-C dimerization. (A) A hypothesized functional complex of SPE-C, MHC-II, and TCR. This model has been built based on the binary complexes of SPE-C/MHC-II (PDB code 1HQR [24]), SPE-C/TCRβ (PDB code 1KTK [41]) and TCRαβ (PDB code 1J8H [15]). Colors are the same as for Color Plate 5 except that SPE-C is colored raspberry and the zinc ion at the SPE-C/MHC-II interface is shown as a light-blue sphere. (B) A possible mode for cross-linking MHC-II at the surface of APCs via SPE-C dimerization. This model has been built using the SPE-C/MHC-II complex along with the SPE-C dimer seen in the crystal structure of SPE-C alone (PDB code 1AN8 [38]).

The putative MHC-II/SPE-C/TCR complex and MHC-II cross-linking by SPE-C dimerization. (A) A hypothesized functional complex of SPE-C, MHC-II, and TCR. This model has been built based on the binary complexes of SPE-C/MHC-II (PDB code 1HQR [24]), SPE-C/TCRβ (PDB code 1KTK [41]) and TCRαβ (PDB code 1J8H [15]). Colors are the same as for Color Plate 5 except that SPE-C is colored raspberry and the zinc ion at the SPE-C/MHC-II interface is shown as a light-blue sphere. (B) A possible mode for cross-linking MHC-II at the surface of APCs via SPE-C dimerization. This model has been built using the SPE-C/MHC-II complex along with the SPE-C dimer seen in the crystal structure of SPE-C alone (PDB code 1AN8 [38]).

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 8 (Chapter 7). Comparison of SAg-MHC class II complexes. (A) Crystal structure of SEB (cyan) interacting with the α-chain of MHC class II (50). (B) Crystal structure of TSST-1 (white) interacting with the α-chain of MHC class II (55). (C) Crystal structure of SPE-C (orange) interacting with the β-chain of MHC class II (64). (D) Crystal structure of SEH (yellow) interacting with the β-chain of MHC class II (82). Residues involved in the SEB-MHC and TSST-1-MHC interactions and residues involved in zinc binding are shown as sticks. The α-chain and the β-chain of MHC class II are dark green and green, respectively. The molecular representations were generated with PyMOL (22).

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Color Plate 8 (Chapter 7). Comparison of SAg-MHC class II complexes. (A) Crystal structure of SEB (cyan) interacting with the α-chain of MHC class II (50). (B) Crystal structure of TSST-1 (white) interacting with the α-chain of MHC class II (55). (C) Crystal structure of SPE-C (orange) interacting with the β-chain of MHC class II (64). (D) Crystal structure of SEH (yellow) interacting with the β-chain of MHC class II (82). Residues involved in the SEB-MHC and TSST-1-MHC interactions and residues involved in zinc binding are shown as sticks. The α-chain and the β-chain of MHC class II are dark green and green, respectively. The molecular representations were generated with PyMOL (22).

Comparison of SAg-MHC class II complexes. (A) Crystal structure of SEB (cyan) interacting with the α-chain of MHC class II (50). (B) Crystal structure of TSST-1 (white) interacting with the α-chain of MHC class II (55). (C) Crystal structure of SPE-C (orange) interacting with the β-chain of MHC class II (64). (D) Crystal structure of SEH (yellow) interacting with the β-chain of MHC class II (82). Residues involved in the SEB-MHC and TSST-1-MHC interactions and residues involved in zinc binding are shown as sticks. The α-chain and the β-chain of MHC class II are dark green and green, respectively. The molecular representations were generated with PyMOL (22).

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 9 (Chapter 7). SAg-MHC class II zinc-dependent interaction site. (A) Zinc-coordination and hydrogen bond pattern in the SEH (yellow)-HLA-DR1 (green)-HA-peptide (magenta) complex (82). (B) Comparison between the SEH (yellow)-HLA-DR1 (green)-HA-peptide (magenta) complex (82) and the SPE-C (orange)-HLA-DR2a (not shown)-MBP-peptide (cyan) complex (64). The molecular representations were generated with PyMOL (22).

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Color Plate 9 (Chapter 7). SAg-MHC class II zinc-dependent interaction site. (A) Zinc-coordination and hydrogen bond pattern in the SEH (yellow)-HLA-DR1 (green)-HA-peptide (magenta) complex (82). (B) Comparison between the SEH (yellow)-HLA-DR1 (green)-HA-peptide (magenta) complex (82) and the SPE-C (orange)-HLA-DR2a (not shown)-MBP-peptide (cyan) complex (64). The molecular representations were generated with PyMOL (22).

SAg-MHC class II zinc-dependent interaction site. (A) Zinc-coordination and hydrogen bond pattern in the SEH (yellow)-HLA-DR1 (green)-HA-peptide (magenta) complex (82). (B) Comparison between the SEH (yellow)-HLA-DR1 (green)-HA-peptide (magenta) complex (82) and the SPE-C (orange)-HLA-DR2a (not shown)-MBP-peptide (cyan) complex (64). The molecular representations were generated with PyMOL (22).

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 10 (Chapter 7). Model of 2MHC-SEA-TCR quaternary complex produced by superposition of the SEH-HLA-DR1 complex (82), the SEA-HLA-DR1 complex (84), and the SPE-C-TCR β-chain complex (99). The α-chain and the β-chain of HLA-DR1 are dark green and green, respectively, SEA is red and the TCR β-chain is blue. The molecular representation was generated with PyMOL (22).

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Color Plate 10 (Chapter 7). Model of 2MHC-SEA-TCR quaternary complex produced by superposition of the SEH-HLA-DR1 complex (82), the SEA-HLA-DR1 complex (84), and the SPE-C-TCR β-chain complex (99). The α-chain and the β-chain of HLA-DR1 are dark green and green, respectively, SEA is red and the TCR β-chain is blue. The molecular representation was generated with PyMOL (22).

Model of 2MHC-SEA-TCR quaternary complex produced by superposition of the SEH-HLA-DR1 complex (82), the SEA-HLA-DR1 complex (84), and the SPE-C-TCR β-chain complex (99). The α-chain and the β-chain of HLA-DR1 are dark green and green, respectively, SEA is red and the TCR β-chain is blue. The molecular representation was generated with PyMOL (22).

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 11 (Chapter 8). (A) Surface representation of a typical staphylococcal/streptococcal superantigen with TCR binding region (green) and MHC class II binding region (red) indicated (front view). (B) Side view of A giving a better picture of the size and position of the TCR binding site. (C) Ribbon diagram of SEA representative of the common structural features of the staphylococcal and streptococcal superantigen family. Blue spheres represent the positions of the two possible zinc sites. The cysteine residues that form the disulfide loop are shown in ball-and-stick representation. (D) The nonclassical superantigen MAM. (E) The nonclassical superantigen YPM.

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Color Plate 11 (Chapter 8). (A) Surface representation of a typical staphylococcal/streptococcal superantigen with TCR binding region (green) and MHC class II binding region (red) indicated (front view). (B) Side view of A giving a better picture of the size and position of the TCR binding site. (C) Ribbon diagram of SEA representative of the common structural features of the staphylococcal and streptococcal superantigen family. Blue spheres represent the positions of the two possible zinc sites. The cysteine residues that form the disulfide loop are shown in ball-and-stick representation. (D) The nonclassical superantigen MAM. (E) The nonclassical superantigen YPM.

(A) Surface representation of a typical staphylococcal/streptococcal superantigen with TCR binding region (green) and MHC class II binding region (red) indicated (front view). (B) Side view of A giving a better picture of the size and position of the TCR binding site. (C) Ribbon diagram of SEA representative of the common structural features of the staphylococcal and streptococcal superantigen family. Blue spheres represent the positions of the two possible zinc sites. The cysteine residues that form the disulfide loop are shown in ball-and-stick representation. (D) The nonclassical superantigen MAM. (E) The nonclassical superantigen YPM.

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 12 (Chapter 8). Schematic diagram illustrating the multiple modes by which superantigens can interact with MHC class II molecules. (A) Conventional peptide antigen. (B) Interaction with a single MHC class II molecule via the generic binding site on the α-chain (e.g., SEB and TSST-1). Interaction of a non-zinc-linked superantigen dimer with two separate MHC class II molecules via the α-chain generic site (e.g., MAM). (C) Interaction of a superantigen with MHC class II β-chain via a high-affinity zinc site and TCR Vβ-chain (e.g., SEC2, SpeA1, and SpeC). (D) Interaction of a superantigen with MHC class II β-chain via a high-affinity zinc site and TCR Vα-chain (e.g., SEH).

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Color Plate 12 (Chapter 8). Schematic diagram illustrating the multiple modes by which superantigens can interact with MHC class II molecules. (A) Conventional peptide antigen. (B) Interaction with a single MHC class II molecule via the generic binding site on the α-chain (e.g., SEB and TSST-1). Interaction of a non-zinc-linked superantigen dimer with two separate MHC class II molecules via the α-chain generic site (e.g., MAM). (C) Interaction of a superantigen with MHC class II β-chain via a high-affinity zinc site and TCR Vβ-chain (e.g., SEC2, SpeA1, and SpeC). (D) Interaction of a superantigen with MHC class II β-chain via a high-affinity zinc site and TCR Vα-chain (e.g., SEH).

Schematic diagram illustrating the multiple modes by which superantigens can interact with MHC class II molecules. (A) Conventional peptide antigen. (B) Interaction with a single MHC class II molecule via the generic binding site on the α-chain (e.g., SEB and TSST-1). Interaction of a non-zinc-linked superantigen dimer with two separate MHC class II molecules via the α-chain generic site (e.g., MAM). (C) Interaction of a superantigen with MHC class II β-chain via a high-affinity zinc site and TCR V-chain (e.g., SEC2, SpeA1, and SpeC). (D) Interaction of a superantigen with MHC class II β-chain via a high-affinity zinc site and TCR V-chain (e.g., SEH).

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 13 (Chapter 14). Superantigen in complex with TCR Vβ chain and MHC class II molecule. (A) Left view. Atomic coordinates of complexes of SEB (red ribbon) with the TCR β-chain (green ribbon) (23) and with HLA DR1 (magenta ribbon) (16) have been superimposed in SEB. (B) Right view and closeup. The antagonist domain in SEB is shown in yellow. Reprinted from Molecular Diversity (17) with permission of the publisher.

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Color Plate 13 (Chapter 14). Superantigen in complex with TCR Vβ chain and MHC class II molecule. (A) Left view. Atomic coordinates of complexes of SEB (red ribbon) with the TCR β-chain (green ribbon) (23) and with HLA DR1 (magenta ribbon) (16) have been superimposed in SEB. (B) Right view and closeup. The antagonist domain in SEB is shown in yellow. Reprinted from Molecular Diversity (17) with permission of the publisher.

Superantigen in complex with TCR Vβ chain and MHC class II molecule. (A) Left view. Atomic coordinates of complexes of SEB (red ribbon) with the TCR β-chain (green ribbon) (23) and with HLA DR1 (magenta ribbon) (16) have been superimposed in SEB. (B) Right view and closeup. The antagonist domain in SEB is shown in yellow. Reprinted from (17) with permission of the publisher.

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 14 (Chapter 14). The antagonist domain is conserved in superantigens. (A) In backbone structures (PDB codes 1SEB, 1SEA, SPEA_STRPY, 1TSS), the domain corresponding to residues SEB150-161 is shown as a magenta ribbon. In SEB, domains that interact with TCR, MHC-II, or both are shown as orange/yellow ribbons. The N-terminal 138 residues in SEB are shown as orange ribbons and cyan strands; corresponding regions in SEA, SPEA, and TSST-1 are cyan. (B) Detail of the 12-amino-acid β-strand/hinge/α-helix antagonist domains that show homology to superantigen antagonist peptide p12. On the right, sequence comparison of p12 with antagonist domains of streptococcal and staphylococcal superantigens is shown. Full amino acid conservation is designated in red, partial conservation in blue. Modified from Nature Medicine (3) with permission of the publisher.

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Color Plate 14 (Chapter 14). The antagonist domain is conserved in superantigens. (A) In backbone structures (PDB codes 1SEB, 1SEA, SPEA_STRPY, 1TSS), the domain corresponding to residues SEB150-161 is shown as a magenta ribbon. In SEB, domains that interact with TCR, MHC-II, or both are shown as orange/yellow ribbons. The N-terminal 138 residues in SEB are shown as orange ribbons and cyan strands; corresponding regions in SEA, SPEA, and TSST-1 are cyan. (B) Detail of the 12-amino-acid β-strand/hinge/α-helix antagonist domains that show homology to superantigen antagonist peptide p12. On the right, sequence comparison of p12 with antagonist domains of streptococcal and staphylococcal superantigens is shown. Full amino acid conservation is designated in red, partial conservation in blue. Modified from Nature Medicine (3) with permission of the publisher.

The antagonist domain is conserved in superantigens. (A) In backbone structures (PDB codes 1SEB, 1SEA, SPEA_STRPY, 1TSS), the domain corresponding to residues SEB is shown as a magenta ribbon. In SEB, domains that interact with TCR, MHC-II, or both are shown as orange/yellow ribbons. The N-terminal 138 residues in SEB are shown as orange ribbons and cyan strands; corresponding regions in SEA, SPEA, and TSST-1 are cyan. (B) Detail of the 12-amino-acid β-strand/hinge/α-helix antagonist domains that show homology to superantigen antagonist peptide On the right, sequence comparison of with antagonist domains of streptococcal and staphylococcal superantigens is shown. Full amino acid conservation is designated in red, partial conservation in blue. Modified from (3) with permission of the publisher.

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 15 (Chapter 14). Accessibility of the antagonist domain in SEB. In the structure of SEB, side chains in the 150-161 β-strand/hinge/α-helix domain are color-coded according to surface accessibility. Dark blue, not exposed; light blue and green, exposed.

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Color Plate 15 (Chapter 14). Accessibility of the antagonist domain in SEB. In the structure of SEB, side chains in the 150-161 β-strand/hinge/α-helix domain are color-coded according to surface accessibility. Dark blue, not exposed; light blue and green, exposed.

Accessibility of the antagonist domain in SEB. In the structure of SEB, side chains in the 150-161 β-strand/hinge/α-helix domain are color-coded according to surface accessibility. Dark blue, not exposed; light blue and green, exposed.

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 16 (Chapter 16). Schematic representation illustrating the differences between conventional peptide antigen presentation and superantigen presentation to MHC class II and TCRs. Conventional antigen is processed by the APC and displayed as discrete peptide fragments within the peptide-binding groove of MHC class II molecules. Superantigens bind to the solvent-exposed face of the MHC class II molecule (α1), forming a bridge between α 1 and TCRVβ.

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Color Plate 16 (Chapter 16). Schematic representation illustrating the differences between conventional peptide antigen presentation and superantigen presentation to MHC class II and TCRs. Conventional antigen is processed by the APC and displayed as discrete peptide fragments within the peptide-binding groove of MHC class II molecules. Superantigens bind to the solvent-exposed face of the MHC class II molecule (α1), forming a bridge between α 1 and TCRVβ.

Schematic representation illustrating the differences between conventional peptide antigen presentation and superantigen presentation to MHC class II and TCRs. Conventional antigen is processed by the APC and displayed as discrete peptide fragments within the peptide-binding groove of MHC class II molecules. Superantigens bind to the solvent-exposed face of the MHC class II molecule (α1), forming a bridge between α 1 and TCRVβ.

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 17 (Chapter 16). Upper panel shows a comparison of the structures of three S. aureus superantigens. Ribbon diagram of crystal structures of SEB (left), SEC3 (center), and TSST-1 (right). The lower panel shows the native folds of the major components of the chimeric proteins, with major SAg contact areas labeled. On the left is a ribbon diagram of the crystal structure of TCRVβ and on the right is a ribbon diagram of the crystal structure of MHC class II DRα1.

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Color Plate 17 (Chapter 16). Upper panel shows a comparison of the structures of three S. aureus superantigens. Ribbon diagram of crystal structures of SEB (left), SEC3 (center), and TSST-1 (right). The lower panel shows the native folds of the major components of the chimeric proteins, with major SAg contact areas labeled. On the left is a ribbon diagram of the crystal structure of TCRVβ and on the right is a ribbon diagram of the crystal structure of MHC class II DRα1.

Upper panel shows a comparison of the structures of three superantigens. Ribbon diagram of crystal structures of SEB (left), SEC3 (center), and TSST-1 (right). The lower panel shows the native folds of the major components of the chimeric proteins, with major SAg contact areas labeled. On the left is a ribbon diagram of the crystal structure of TCRVβ and on the right is a ribbon diagram of the crystal structure of MHC class II DRα1.

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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Image of Color Plate 18 (Chapter 16). Comparison of the minimized average structures of the superantigen-chimera complexes. (A) SEB-chimera complex. (B) SEC3-chimera complex. (C) TSST-1-chimera complex. The superantigen is orange, the DRα1 is yellow, the TCRVβ is blue, and the linker is green.

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Color Plate 18 (Chapter 16). Comparison of the minimized average structures of the superantigen-chimera complexes. (A) SEB-chimera complex. (B) SEC3-chimera complex. (C) TSST-1-chimera complex. The superantigen is orange, the DRα1 is yellow, the TCRVβ is blue, and the linker is green.

Comparison of the minimized average structures of the superantigen-chimera complexes. (A) SEB-chimera complex. (B) SEC3-chimera complex. (C) TSST-1-chimera complex. The superantigen is orange, the DRα1 is yellow, the TCRVβ is blue, and the linker is green.

Citation: Kotb M, Fraser J. 2007. Color Plates, In Superantigens. ASM Press, Washington, DC.
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