Structural Maintenance of Chromosomes (SMC) proteins play fundamental roles in many aspects of chromosome organization and dynamics. The SMC complexes form unique structures with long coiled-coil arms folded at a hinge domain, so that the globular N- and C-terminal domains are brought together to form a "head". Within the Smc5/6 complex, we previously identified two subcomplexes containing Smc6-Smc5-Nse2 and Nse1-Nse3-Nse4. A third subcomplex containing Nse5 and 6 has also been identified recently. We present evidence that Nse4 is the kleisin component of the complex, which bridges the heads of Smc5 and 6. The C-terminal part of Nse4 interacts with the head domain of Smc5 and structural predictions for Nse4 proteins suggest similar motifs that are shared within the kleisin family. Specific mutations within a predicted winged helix motif of Nse4 destroy the interaction with Smc5. We propose that Nse4 and its orthologs form the d-kleisin subfamily. We further show that Nse3, as well as Nse5 and Nse6 also bridge the heads of Smc5 and 6. The Nse1-3-4 and Nse5-6 subcomplexes bind to the Smc5-6 heads domain at different sites.