A T cell receptor flattens a bulged antigenic peptide presented by a major histocompatibility complex class I molecule Fleur E Tynan 1,5 , Hugh H Reid 1,5 , Lars Kjer-Nielsen 2 , John J Miles 3 , Matthew C J Wilce 1 , Lyudmila Kostenko 2 , Natalie A Borg 1 , Nicholas A Williamson 4 , Travis Beddoe 1 , Anthony W Purcell 4 , Scott R Burrows 3 , James McCluskey 2 & Jamie Rossjohn 1 Plasticity of the T cell receptor (TCR) is a hallmark of major histocompatibility complex (MHC)–restricted T cell recognition. However, it is unclear whether interactions of TCR and peptide–MHC class I (pMHCI) always conform to this paradigm. Here we describe the structure of a TCR, ELS4, in its non-ligand-bound form and in complex with a prominent ‘bulged’ Epstein-Barr virus peptide bound to HLA-B*3501. This complex was atypical of previously characterized TCR-pMHCI interactions in that a rigid face of the TCR crumpled the bulged antigenic determinant. This peptide ‘bulldozing’ created a more featureless pMHCI determinant, allowing the TCR to maximize MHC class I contacts essential for MHC class I restriction of TCR recognition. Our findings represent a mechanism of antigen recognition whereby the plasticity of the T cell response is dictated mainly by adjustments in the MHC-bound peptide. Clonotypic ab T cell receptors (TCRs) expressed on the surfaces of CD8 + cytotoxic T lymphocytes (CTLs) recognize peptide fragments bound to major histocompatibility complex (MHC) class I molecules (pMHCI) 1–3 . The specificity of the TCR repertoire is refined during thymic development and, after positive and negative selection, approximately 1  10 8 TCRs remain 4 . TCRs are inherently cross- reactive, and that degeneracy, coupled with the diversity of the TCR repertoire, is required for recognition of the potentially infinite number of pMHC ligands 5 . Structural and biophysical studies of TCR-pMHCI interactions have provided an understanding of the basis for plasticity at this interface 6–13 . First, comparison of the available TCR structures, unbound and bound to pMHCI complexes, has demonstrated that TCR complementarity-determining regions (CDRs) undergo confor- mational changes upon recognition of pMHCI (refs. 6,14). CDR conformational changes upon mainly in the hypervariable CDR3 loops, although the CDR1 and CDR2 loops of a TCRa chain can also undergo conformational changes upon ligation to pMHCI (ref. 8). Second, comparison of TCR structures bound to altered peptide ligands has demonstrated the malleability of the CDR3 loops in accommodating variations in the peptide ligand 15,16 . Third, struc- tural comparison of a single TCR bound to different pMHCI ligands has shown that the degeneracy of TCR recognition lies mainly in the ability of the CDR3 loops to undergo conformational change 7,11,17 . These studies have shown that TCRs can mold around a given pMHCI ‘landscape’ to enable optimal interaction. TCR-pMHCI interactions are of relatively weak affinity and are characterized by slow ‘on rates’ and fast ‘off rates’ 18 . In almost all TCR-pMHCI interactions characterized so far, the pMHCI has moved minimally, if at all, upon TCR engagement. Small conformational changes have been found in side-chain movements of MHC class I residues and modest, if any, changes have been found in the peptide conformation. One exception is the A6 TCR–HLA-A2–Tax system 19–21 , in which a region of the bound peptide undergoes modest conformational changes upon TCR ligation. However, the magnitude of the conformational change in the peptide that can be attributed to TCR docking is uncertain, given that the peptide in the binary complex participates in crystal contacts. Those principles of ‘static’ pMHCI complexes have been developed mainly from studies of TCR interactions with pMHCI structures containing canonical peptides eight to nine amino acids in length. The function of atypically long peptide determinants (over ten amino acids) in MHC class I–restricted T cell–mediated immunity is becoming evident 22 . Generally, long peptides bulge centrally from MHC class I molecules and show varying degrees of mobility. Consequently, such bulged epitopes may represent challenges for © 2007 Nature Publishing Group http://www.nature.com/natureimmunology Received 5 October 2006; accepted 20 December 2006; published online 28 January 2007; doi:10.1038/ni1432 1 The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia. 2 Department of Microbiology & Immunology, University of Melbourne, Parkville, Victoria 3010, Australia. 3 Cellular Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, 4029, Australia. 4 Department of Biochemistry, University of Melbourne, Parkville, Victoria 3010, Australia. 5 These authors contributed equally to this work. Correspondence should be addressed to J.M. (jamesm1@unimelb.edu.au) or J.R. (jamie.rossjohn@med.monash.edu.au). NATURE IMMUNOLOGY ADVANCE ONLINE PUBLICATION 1 ARTICLES