UMMS Affiliation

Program in Molecular Medicine; Department of Pathology

Publication Date


Document Type



Amino Acids, Peptides, and Proteins | Computational Biology | Immunology of Infectious Disease | Immunopathology | Infectious Disease | Virology | Virus Diseases | Viruses


The T cell receptor (TCR) repertoire is an essential component of the CD8 T-cell immune response. Here, we seek to investigate factors that drive selection of TCR repertoires specific to the HLA-A2-restricted immunodominant epitope BRLF1109-117 (YVLDHLIVV) over the course of primary Epstein Barr virus (EBV) infection. Using single-cell paired TCRalphabeta sequencing of tetramer sorted CD8 T cells ex vivo, we show at the clonal level that recognition of the HLA-A2-restricted BRLF1 (YVL-BR, BRLF-1109) epitope is mainly driven by the TCRalpha chain. For the first time, we identify a CDR3alpha (complementarity determining region 3 alpha) motif, KDTDKL, resulting from an obligate AV8.1-AJ34 pairing that was shared by all four individuals studied. This observation coupled with the fact that this public AV8.1-KDTDKL-AJ34 TCR pairs with multiple different TCRbeta chains within the same donor (median 4; range: 1-9), suggests that there are some unique structural features of the interaction between the YVL-BR/MHC and the AV8.1-KDTDKL-AJ34 TCR that leads to this high level of selection. Newly developed TCR motif algorithms identified a lysine at position 1 of the CDR3alpha motif that is highly conserved and likely important for antigen recognition. Crystal structure analysis of the YVL-BR/HLA-A2 complex revealed that the MHC-bound peptide bulges at position 4, exposing a negatively charged aspartic acid that may interact with the positively charged lysine of CDR3alpha. TCR cloning and site-directed mutagenesis of the CDR3alpha lysine ablated YVL-BR-tetramer staining and substantially reduced CD69 upregulation on TCR mutant-transduced cells following antigen-specific stimulation. Reduced activation of T cells expressing this CDR3 motif was also observed following exposure to mutated (D4A) peptide. In summary, we show that a highly public TCR repertoire to an immunodominant epitope of a common human virus is almost completely selected on the basis of CDR3alpha and provide a likely structural basis for the selection. These studies emphasize the importance of examining TCRalpha, as well as TCRbeta, in understanding the CD8 T cell receptor repertoire.


Cytotoxic T cells, T cells, Sequence motif analysis, T cell receptors, Crystal structure, Cell staining, Cloning, Sequence analysis, UMCCTS funding

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Copyright: © 2019 Kamga et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium,provided the original author and source are credited

DOI of Published Version



PLoS Pathog. 2019 Nov 25;15(11):e1008122. doi: 10.1371/journal.ppat.1008122. [Epub ahead of print] Link to article on publisher's site

Journal/Book/Conference Title

PLoS pathogens

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Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.