V. Antigen Binding Site

Like the antigen combining site of immunoglobulins, the TCR binding site is composed of six complementarity-determining regions (CDRs). Because of the specificity of the TCR for MHC and peptide ligand, however, the antigen combining site of the TCR is uniquely evolved to meet its dual function. Unlike antibodies, which exhibit a wide variety of surface topologies to match various protein, carbohydrate and lipid antigens, the binding site of the TCR is essentially flat. It is designed to accommodate MHC recognition by four of the CDRs, with the two most variable CDRs left to discriminate between bound peptides.

The alpha chain in the 2C TCR is composed of the Vα3, Jα58, and Cα gene segments (residues 1-93, 94-112, and 113-202, respectively). Both CDR1 (24-31α) and CDR2(48-55α) are contained within the Vα3 gene segment, so their variability is restricted by the number of Vα segments in the genome. CDR3 (93-104α), however, lies at the V-J junction, and has the potential for sequence variation from all V and J segments, as well as the diversity created by the addition or subtraction of nucleotides at the V-J junction. It is CDR3, therefore, that carries the bulk of the sequence variation in the alpha chain.

The beta chain in the 2C TCR is composed of the Vβ8.2, Dβ2, Jβ2.4, and Cβ2 gene segments (residues 1-94, 95-97, 98-110, and 111-237, respectively). As in the alpha chain, CDR1 (26-31β) and CDR2 (48-55β) are wholly contained within the Vβ8.2 gene segment. In the beta chain, however, CDR3 (95-107β) contains two junctions (V-D and D-J), and thus has even greater sequence variation, bearing the majority of sequence diversity in the TCR.

One remarkable feature of the TCR binding site is its relatively flat topology: it is without any major clefts or protrusions (except at its center), and contains only five charged residues on the exposed surface. The four corners of the antigen-combining site are defined by CDR1α, CDR2α, CDR1β, and CDR2β. These loops are anchored within the framework of the alpha and beta variable domains, and thus maintain a fixed position. They are composed primarily of small-sidechain amino acids, except for six tyrosine residues which are bent to lie flat against the molecule. The fixed, uniform position of CDRs 1 and 2 at the edges of the binding site allows these loops to define the orientation of the TCR-MHC complex. In general, these pseudo-variable CDRs interact with the helices and outer edges of the MHC peptide-binding groove, leaving CDR3 to specifically bind the antigenic peptide.

Unlike CDRs 1 and 2, the alpha and beta CDR3 loops lie at the Vα-Vβ interface, and thus are not constrained within the framework of the immunoglobulin-type fold. The two CDR3 loops are stabilized by a symmetric hydrophobic interaction at their base (Leu104α-Leu106β), leaving a narrow hydrophobic cleft between the two at the center of the binding site. This cleft comprises one of two major topological features of the binding site; the other is the full extension of Phe100α from the tip of CDR3α. Both of these features may be designed to accommodate the hydrophobic sidechains of a peptide in the MHC binding groove. It is both the increased sequence diversity and greater conformational freedom of the CDR3 loops that govern specific binding of the TCR to antigenic peptides in the context of MHC presentation.