The 2.0-Å resolution crystal structure of a trimeric antibody fragment with noncognate V(H)–V(L) domain pairs shows a rearrangement of V(H) CDR3

The 2.0-Å resolution x-ray crystal structure of a novel trimeric antibody fragment, a “triabody,” has been determined. The trimer is made up of polypeptides constructed in a manner identical to that previously described for some “diabodies”: a V(L) domain directly fused to the C terminus of a V(H) domain—i.e., without any linker sequence. The trimer has three Fv heads with the polypeptides arranged in a cyclic, head-to-tail fashion. For the particular structure reported here, the polypeptide was constructed with a V(H) domain from one antibody fused to the V(L) domain from an unrelated antibody giving rise to “combinatorial” Fvs upon formation of the trimer. The structure shows that the exchange of the V(L) domain from antibody B1-8, a V(λ) domain, with the V(L) domain from antibody NQ11, a V(κ) domain, leads to a dramatic conformational change in the V(H) CDR3 loop of antibody B1-8. The magnitude of this change is similar to the largest of the conformational changes observed in antibody fragments in response to antigen binding. Combinatorial pairing of V(H) and V(L) domains constitutes a major component of antibody diversity. Conformationally flexible antigen-binding sites capable of adapting to the specific CDR3 loop context created upon V(H)–V(L) pairing may be employed by the immune system to maximize the structural diversity of the immune response.