Structural basis of nucleosome binding and SMARCB1 displacement by SSX1/2 disordered domains

Synovial sarcoma is driven by the SS18–SSX fusion oncoprotein, in which the SSX C-terminal region replaces SMARCB1 in the BAF chromatin remodeling complex. However, the structural basis by which SSX displaces SMARCB1, and the potential functional differences between SSX1 and SSX2 have remained unclear. Here, we determined cryo-electron microscopy structures of SSX1RD– and SSX2RD–unmodified nucleosome complexes at a resolution of 2.4 Å and 2.5 Å, respectively. Both structures revealed conserved interactions mediated by the SSX RLR motif with the acidic patch, a cation–π interaction between W164 and R167, and insertion of Y177 into a hydrophobic pocket of H2A, indicating that SSX1RD and SSX2RD are functionally interchangeable in nucleosome binding. Molecular dynamics simulations and binding free-energy analyses showed that SSXRD binds the acidic patch more strongly than SMARCB1, explaining how SSX fusion proteins displace SMARCB1 during BAF assembly. Complementary circular dichroism and NMR spectroscopy confirmed that SSX1(111–188) and SSX2(111–188) are intrinsically disordered regions capable of weak nucleosome binding and nuclear condensates formation. Together, these findings establish a mechanistic and structural framework for understanding SSX-driven chromatin remodeling, offering a basis for therapeutic strategies targeting SSX-mediated BAF dysregulation in synovial sarcoma.