Structural Basis for Unusual TCR CDR3β Usage Against an Immunodominant HIV-1 Gag Protein Peptide Restricted to an HLA-B*81:01 Molecule

Abstract

In HIV infection, some closely associated human leukocyte antigen (HLA) alleles are correlated with distinct clinical outcomes although presenting the same HIV epitopes. The mechanism that underpins this observation is still unknown, but may be due to the essential features of HLA alleles or T cell receptors (TCR). In this study, we investigate how T18A TCR, which is beneficial for a long-term control of HIV in clinic, recognizes immunodominant Gag epitope TL9 (TPQDLTML180-188) from HIV in the context of the antigen presenting molecule HLA-B*81:01. We found that T18A TCR exhibits differential recognition for TL9 restricted by HLA-B*81:01. Furthermore, via structural and biophysical approaches, we observed that TL9 complexes with HLA-B*81:01 undergoes no conformational change after TCR engagement. Remarkably, the CDR3β in T18A complexes does not contact with TL9 at all but with intensive contacts to HLA-B*81:01. The binding kinetic data of T18A TCR revealed that this TCR can recognize TL9 epitope and several mutant versions, which might explain the correlation of T18A TCR with better clinic outcomes despite the relative high mutation rate of HIV. Collectively, we provided a portrait of how CD8⁺ T cells engage in HIV-mediated T cell response.

Keywords: CD8+ T cells; HIV; HLA; T cell receptor; antigen presentation.

Figure 1

The structure of T18A TCR/HLA-B*81:01/TL9 complex. (A) The T18A TCR (T18Aα in pale pink, T18Aβ in pale cyan) recognize TL9 epitope presented by HLA-B*81:01. (B) The footprint of T18A TCR on the surface of HLA-B*81:01-TL9 complex. (C P Pie charts show the contribution of TCR segments toward the pHLA complex. (D) Interactions of TCR towards peptide. (E) Detailed interactions of T18A TCR with Gag-TL9 epitope in the context of HLA-B*81:01. Blue dashes denote hydrogen bonds; peptide amino acids are indicated in single-letter abbreviations and TCR residues are labeled in three-letter abbreviations. The colors correspond to TCR segment showed in pie chat. (F) Refined maps (2Fo-Fc) of the peptide in HLA-B complexes. The HLA molecules are represented in cartoon, and the peptides are represented as stick.

Figure 2

HLA-B*81:01/TL9 complex binds to T18A TCR with no conformational change. (A) the conformational change of HLA-B*81:01/TL9 complex after T18A TCR engagement. (B, C) the interactions between T18A TCR and HLA-B*81:01/TL9 complex. TPQDLNTML peptide presented by HLA-B*81:01 (PDB: 4U1I) in peptide-MHC complexes.

Figure 3

The rare docking mode of T18A CDR3β on α2 helix of the HLA but not the peptide. The foot print of TCR CDR3β on p-MHC complexes are colored in yellow from 5 different recognition profiles. (A) The foot print of T18A TCR CDR3β on p-HLA complex. (B–E) CDR3β use in other 4 structures, C12C TCR (PDB: 4G8G), F24 TCR (PDB: 6CQL), KK50.4 TCR (PDB: 2ESV) and DM1 TCR (PDB: 3DXA). Peptide in each panel is shown in stick, CDR loops are shown in cartoon, and MHCs are shown in surface view.

Figure 4

The uncommon “opened” T18A CDR3α alters the relative orientation of Vα to Vβ. (A) The “opened” conformation of the β sheet interactions between Vα and Jα of T18A when it is bound to B8101-pTL9. A stick representation of the protein backbone and the side chains of the FGXG conserved motif are shown. Backbone H-bonds, as well as H-bond with R93, are shown in green. (B) The “closed” conformation of Vα-Jα interactions of C12C TCR (PDB: 4G8G) and 1E6 TCR (PDB: 3UTS), representing traditional CDR3α conformation in most of TCR-pMHC profiles. (C) The disruption of Vα-Jα H bonds of YAe62 (PDB: 3C60) when it is bound to MHC II versus MHC I, indicating the alteration of CDR3α could expand the ability of the TCR to adapt Different MHC Ligands. (D) The Vα and Vβ domains of T18A and 1E6 TCR are overlaid by Vβ as similar TRBV gene is used. (E) A view looking down through the TCR is shown. Relative position of CDRα loops to CDRβ loops are changed due to “opened” or “closed” CDR3α. The relative distance and angle of movement is indicated.

Figure 5

High-affinity T18A TCR bind to TL9 or TL9 escape variants under HLA-B*81:01 restriction. (A) SPR binding data for T18A TCR recognition of the wildtype (WT) and popular mutated TL9 presented by HLA-B*81:01. KD values range from 4.7 μM for the WT TL9 peptide to >250 μ M for the TPsDLNsML peptide. (B) HLA-associated variation of TL9-Gag in B8101-positve HIV infected patients. (C) Different escape modes in TL9 epitope are illustrated as Sequence Logo, demonstrating TL9 mutation in B8101 background is located at position 3 and 7.