Three neurotrophic factors, brain-derived neurotrophic factor (BDNF), neurotrophin-3 (NT-3), and nerve growth factor (NGF) form noncovalent homodimers in solution. Since they are highly homologous proteins, it seemed probable that two monomers of these proteins might associate together to form a heterodimer. This was tested by denaturing the two different proteins together in 6 M guanidine HCl and refolding them in phosphate-buffered saline. When the refolded mixture of BDNF and NT-3 was subjected to Mono S cation exchange chromatography, a new peak was observed eluting between NT-3 and BDNF, which accounted for about 30% of the protein used. This new protein species migrated as a single band upon native gel electrophoresis with mobility between that of the NT-3 homodimer and the BDNF homodimer, indicating that a complex had been formed. Sedimentation equilibrium data show that the dissociation constant of this heterodimer is < 3 x 10(-10) M. The heterodimer was stable upon incubation at 37 degrees C in phosphate-buffered saline over 11 days. Having determined that the heterodimer is highly stable, it was subjected to various biological assays. Autophosphorylation assay using TrkB receptor showed that the heterodimer is indistinguishable from the BDNF or NT-3 homodimer in the ability to induce phosphorylation of the receptor. It was also indistinguishable from the homodimers in the neurotrophic activity using chick dorsal root ganglion explant. In the sympathetic neuron survival assay, the heterodimer behaved more similarly to NT-3, whereas in the dopamine uptake assay, it was intermediate between the two homodimers. In addition, the heterodimer was shown to be retrogradely transported in the dorsal root ganglion neurons. A heterodimer between NGF and BDNF is formed but much less effectively than the NT-3.BDNF heterodimer, and it is not stable even at 4 degrees C. These results indicate that BDNF and NT-3 have an intersubunit contact surface for dimerization resembling each other's but different from the contact surface of NGF.