Fig 1.
Cuboid and grid representations of the T–cell receptor geometries.
(A) Localisation of the considered Vα and Vβ variable domains within the ternary TCR:pMHC complex. A TCR consists of two chains, the α and the β chain (blue and red). Each chain is partitioned into two domains, the constant domain (Cα and Cβ shown transparently) and a variable domain (Vα and Vβ, here surrounded by cuboids). The Vα and Vβ domains form the binding interface to the major histocompatibility complex (MHC) molecule (green) presenting an antigenic peptide (magenta) to the TCR. This work focuses on the variable domains. (B) Superimposition of the TCR variable domains. (i) The TCR structures were superimposed on the Vα domains leading to displaced Vβ domains. (ii) Cuboids were placed around the superimposed Vα and Vβ domains. This unified description of the different domains allows a quantitative analysis of the displacement. (C) Preparation of the cuboid placement templates. Vα (blue) and Vβ (red) domains of the structure 2bnu are used as reference structure. Both chains are surrounded with cuboids of the size of their spatial extent. Residues considered for superimposition are determined in an iterative process (unused residues are depicted transparently). These residues are used to compute the angular displacement of the Vβ domain relative to the Vα domain. (D) Center of Rotation (CoR). (i) Different geometries of (only three for clearness) β-cuboid geometries (red), superimposed on the α-cuboids (blue). (ii) Grids were fit into the β-cuboids. (iii) For each grid point i, the sum of pairwise distances and the variance was computed according to Formula 2. (iv) The residues at the center of rotation (CoR, green sphere) were investigated. For most of the structures, a conserved pair hydrogen bond interaction between the α and the β chain is located directly at the CoR. These hydrogen bonds are established by conserved Q residues.
Fig 2.
Differences in the TCR chain association geometries.
(A) Differences between the bound and unbound geometries. Shown are seven different receptor types in their unbound state as well as their bound state. Notably, for the 1G4 receptor the two unbound states are derived from different crystal structures, but are very similar. For some receptors, such as the 2C receptor, crystal structures including different ligands are available. In case of the 2C TCR, wild type (wt), 2C T7 and 2C T7 mutants are shown. In case of the E8 TCR, the two unbound states are derived from the same crystal structure. (B) Different conformations of the bound 2C TCR structures and their variants. The magnifications show the different CDR1/3 conformations observed in the m67 variant structure 2e2h (green), with respect to the 2C T7 variants (right, blue, 2oi9, 3e3q, and 2e7l) and the 2C wt structures (left, blue, 1g6r, 1mwa, and 2ckb). In the lower figures both variable domains are shown together with the placed cuboids for the structures 2e2h (m67, green, left+right) in comparison to 2e7l (T7 m6, blue/red, right) and 1mwa (2C wt, blue/red, left). The αCDR3 loops of the T7 variants differ in sequence and thus in their backbone conformations, whereas the CDR1 loop conformation is the same for the T7-wt, m6, and m13, but differs for m67 (upper left magnification). In the case of the m67 variant the CDR3 and CDR1 loop conformations are consistent with the 2C wt conformations (upper right magnification).
Table 1.
All TCR structures used for the analysis.
Fig 3.
Geometry clusters of pMHC bound TCRs.
Pairwise Euler-angle distances (EAD) were determined for all pMHC-bound TCR structures according to Formula 1. The distance matrix was hierarchically clustered using the Ward update formula. We identified six significant clusters, using a bootstrapping approach [58]. Notably, in most of the cases, TCRs of the same type occur in the same cluster. Upper panel: Clustering dendrogram with bootstrapping results (au = approximately unbiased, bp = bootstrapping probability). Left panel: TCR types occurring within a cluster. Right/lower panel: PDB identifiers and corresponding TCR names. Central panel: Pairwise Euler-angle distances (EAD). The color key is provided in the bottom of the figure.
Table 2.
Conservation at the CoR position.
Fig 4.
Exceptional structural examples of the center of rotation.
Region around the Center of Rotation (CoR), the Vα domain is shown in blue and the Vβ domain in red. Hydrogen atoms were added for the end-groups of the interacting amino acids. The average center of rotation is drawn as an orange sphere and the interacting residues are shown in licorice representation. CoR stabilizing interactions are drawn as a green line. For these six structures the highly conserved Q-Q interaction between the α and the β chains is replaced by the following residues (shown in licorice style): (A, D-F) αK (PDB-IDs: 1bd2, 3qiu, 3qiw, 3qjh), (B) βR (PDB-ID: 2esv), (C) αW (PDB-ID: 3gsn).
Table 3.
Pairwise Euler Angle Distances [°] of the bound and free 2C TCR variants.
Table 4.
Pairwise Euler Angle Distances [°] of the bound and free 1G4 TCR variants.