T cell antigen receptor (TCR) triggering determines the fate of immature thymocytes. The affinity of the TCR for its endogenous peptide͞MHC ligands serves as a signal for positive or negative selection through mechanisms that are still little understood. We have used a conformation-specific antibody to demonstrate that recognition of TCR ligands that lead to negative selection induces a conformational change in the TCR in situ. In contrast, this conformational change is elicited in only a small percentage of immature thymocytes during positive selection. Using a TUNEL assay, we demonstrate that the conformational change in the TCR is strongly linked to activation of programmed cell death in conditions leading to negative selection. Furthermore, the few conformational change-positive thymocytes detected in conditions that preferably lead to positive selection are also TUNELpositive. Thus, the conformational change in the TCR may underlie the discrimination of ligands leading to positive and negative selection.signal transduction ͉ thymic differentiation ͉ negative selection T he T cell antigen receptor (TCR) complex is composed in most T cells of the ligand-binding TCR␣ and TCR subunits and the signal-transducing CD3␥, CD3␦, CD3 , and CD3 (CD247) (1, 2). The differentiation of T cells is controlled by the transduction of pre-TCR and TCR signals. Differentiation of immature CD4 ϩ CD8 ϩ double-positive (DP) to mature CD4 ϩ or CD8 ϩ single-positive thymocytes is initiated when the TCR-␣ heterodimer engages the peptide͞MHC (pMHC) (2). A unique feature of the TCR is its ability to scan structurally similar pMHC ligands and transmit distinct biochemical signals depending on the strength of the ligand recognized (3, 4). In developing thymocytes, weak TCR ligands induce positive selection, and stronger ligands induce negative selection (5). However, mature T cells are tolerant to weak TCR ligands in the periphery, and they respond to strong ligands by activating a program of cell proliferation and cell differentiation. The differential responsiveness of immature and mature T cells to weak ligands constitutes the cornerstone of self-tolerance that is acquired in the thymus.Many studies have focused on how the TCR␣ heterodimer communicates ligand engagement to the CD3 subunits, how the CD3 subunits translate this information into a specific cellular response, and how the TCR complex discriminates between strong and weak ligands. The engagement of the TCR with a weak ligand in mature T cells results in a distinct pattern of intracellular signaling compared with that induced by a full-agonist peptide. For example, stimulation with a weak ligand induces only partial phosphorylation of the CD3 and CD3 chains and the recruitment, but not the phosphorylation, of the -associated protein of 70 kDa, ZAP70 (6, 7). Hence, weak ligands activate only a subset of the downstream signaling pathways that are activated by an agonist peptide (8). Weak ligands bind to the TCR with a lower affinity and a higher dissociation rate than full a...