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1 Supplementary Information Two common structural motifs for TCR recognition by staphylococcal enterotoxins Karin Erica Johanna Rödström 1, Paulina Regenthal 1, Christopher Bahl 2, Alex Ford 2, David Baker 2, Karin Lindkvist-Petersson 1 1. Department of Experimental Medical Science, Lund University, BMC C13, , Lund, Sweden. 2. Department of Biochemistry, University of Washington, and Howard Hughes Medical Institute, Seattle, Washington 98195, USA. 1
2 Supplementary Figures Figure S1. Structure of the SEE-TCR Complex. The present structure (PDB ID: 5FKA) (coloured) compared to the previously published SEE-TCR structure (PDB ID: 4UDU) (grey) (A) Overall structure of SEE-TCR, with SEE shown in beige, and TCR in purple and blue for the α- and β-chain, respectively. Close-up of the SEE α2-helix (B) and contacting residues in TCR, the hydrophobic patch, consisting of the β2-β3 and β4-β5a loops (C), the α4-β9 loop (D), (E) and the upper part of the α5-helix. Hydrogen bonds are marked as dotted lines and residues designated as s for SAg and b for TRBV7-9. 2
3 Figure S2. Stereo view of the 2Fo-Fc electron density maps of the structures. (A) SEAF47ATCR with SEA in green, TCRα in purple and TCRβ in blue. (B) SEE-TCR, with SEE in beige, TCRα in purple and TCRβ in blue. Structures are shown in stick representation, with the 2FoFc maps contoured at 1.0σ. 3
4 Figure S3. View of the SAg-TCR interfaces. The 2Fo-Fc electron density maps contoured at 1.0σ are shown around interface residues in the (A) SEA F47A -TCR and (B) SEE-TCR structures. Residues designated as s for SAg and b for TRBV7-9. 4
5 Figure S4. Alignment of the SAgs and TRBV/TRAVs investigated. (A) Superantigens SEB, SEC3, SEE, and SEH are aligned with respect to SEA (B) The htrbv7-9, mtrbv 13-3 and htrav27 aligned with respect to htrbv7-9 in the SEAF47A-TCR structure. Alignments were performed using secondary structure matching and RMSD values are shown in Supplementary Table S3. 5
6 Supplementary Tables Table S1. Intermolecular Hydrogen Bonds in the SEE-TCR Structure. Residue Residue Distance Atom Atom SEE TRBV [Å] Asn21 Oδ1 Gln55 Oε1 3.0 Asn21 Nδ2 Leu56 O 3.2 Ser24 Oγ Gln55 Nε2 2.9 Asn25 Oδ1 Gln55 N 2.8 Asn25 Nδ2 Gln55 O 3.1 Arg27 Nη2 Ser67 Oγ 3.1 Gln28 Nε2 Arg70 O 3.0 Tyr32 Oη Glu69 Oε2 2.9 Trp63 Nε1 His30 O 3.1 Tyr64 Oη Asn52 Nδ2 2.9 Tyr64 Oη Glu53 Oε1 3.0 Tyr64 Oη Glu53 Oε2 2.9 Gly93 N Glu53 Oε1 3.0 Ser174 O Gln81 Nε2 3.1 Ser174 Oγ Asp64 O 2.7 Tyr205 Oη Leu56 O 2.6 Table S2. Intermolecular Van der Waals Contacts (distances less than 4 Å) in the SEA F47A - TCR and SEE-TCR Complexes. SEA TCR SEE TCR Thr21 Ser28 Arg20 Ser28 Asn25 Glu29 Asn21 Glu29 Lys27 His30 Ser24 His30 Gln28 Gln51 Asn25 Asn31 Tyr32 Asn52 Arg27 Gln51 Glu34 Glu53 Gln28 Asn52 Ser62 Ala54 Tyr32 Glu53 Trp63 Gln55 Asn33 Ala54 Tyr64 Leu56 Pro62 Gln55 Tyr92 Asp64 Trp63 Leu56 Gly93 Arg65 Tyr64 Glu57 Tyr94 Ser67 Tyr91 Lys58 Val174 Glu69 Tyr92 Asp64 Phe175 Arg70 Gly93 Arg65 Tyr205 Pro71 Tyr94 Phe66 Ser206 Lys72 Ser174 Ser67 Gly73 Phe175 Ala68 Ser74 Tyr205 Glu69 Gln81 Pro206 Arg70 Pro71 Ser74 Glu79 Gln81 6
7 Table S3. Pairwise RMSD values (Å) between SAgs (chain IDs B or C) and variable TCR domains (chain IDs A or B), calculated using secondary structure matching. SAg SEA 5FK9 (C) SEB 1SBB (B) SEC3 3BYT (B) SEE 5FKA (C) SEH 2XNA (C) TRBV/TRAV htrbv7-9 5FK9 (B) mtrbv13-2 1SBB (A) mtrbv13-2 3BYT (A) htrbv7-9 5FKA (B) htrav27 2XNA (B) SEA 5FK9 (C) htrbv7-9 5FK9 (B) SEB 1SBB (B) SEC3 3BYT (B) SEE 5FKA (C) SEH 2XNA (C) mtrbv13-2 1SBB (A) mtrbv13-2 3BYT (A) htrbv7-9 5FKA (B) htrav27 2XNA (B) Table S4. Equilibrium Dissociation Constants for the Studied Staphylococcal Enterotoxins to TCR. SAg TCR Kd [μm] Reference SEA htrbv Hedlund et al. (2013) 1 SEE htrbv7-9 6 Hedlund et al. (2013) 1 SEB mtrbv Malchiodi et al. (1995) 2 SEB htrbv Rodstrom et al. (2014) 3 SEC3 mtrbv Leder et al. (1998) 4 SEH htrav27 4 Pumphrey et al. (2007) 5 7
8 Table S5. Residues in TCR Affected by in Silico Alanine-scanning Mutagenesis with ΔΔG complex values shown in kcal/mol. SEA-hTRBV7-9 SEE-hTRBV7-9 Residue ΔΔGcomplex Residue ΔΔGcomplex Glu Asn Gln Glu Leu Leu Gln Glu Gln SEB-mTRBV13-2 SEC3-mTRBV13-2 Residue ΔΔGcomplex Residue ΔΔGcomplex - - Lys SEB-hTRBV19 SEH-hTRAV27 Residue ΔΔGcomplex Residue ΔΔGcomplex Tyr Val Gln Arg Ile Phe Supplementary References 1 Hedlund, G. et al. The tumor targeted superantigen ABR selectively engages TRBV7-9 and exploits TCR-pMHC affinity mimicry in mediating T cell cytotoxicity. PloS one 8, e79082, doi: /journal.pone (2013). 2 Malchiodi, E. L. et al. Superantigen binding to a T cell receptor beta chain of known three-dimensional structure. The Journal of experimental medicine 182, (1995). 3 Rodstrom, K. E., Elbing, K. & Lindkvist-Petersson, K. Structure of the superantigen staphylococcal enterotoxin B in complex with TCR and peptide-mhc demonstrates absence of TCR-peptide contacts. J Immunol 193, , doi: /jimmunol (2014). 4 Leder, L. et al. A mutational analysis of the binding of staphylococcal enterotoxins B and C3 to the T cell receptor beta chain and major histocompatibility complex class II. The Journal of experimental medicine 187, (1998). 5 Pumphrey, N. et al. Cutting edge: Evidence of direct TCR alpha-chain interaction with superantigen. J Immunol 179, , doi:179/5/2700 [pii] (2007). 8
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