The synaptonemal complex (SC) transiently stabilizes pairing interactions between homologous chromosomes during meiosis. Assembly of the SC is mediated through integration of opposing transverse filaments (TF) into a central element (CE), a process that is poorly understood. We have here analyzed the localization of the TF protein SYCP1 and the CE proteins SYCE1, SYCE2 and SYCE3 within the central region of the SC in mouse spermatocytes using immunoelectron microscopy. Distribution of immuno-gold particles in a lateral view of the SC, supported by protein interaction data, suggest that the N-terminal region of SYCP1 and SYCE3 form a joint bilayered central structure and that SYCE1 and SYCE2 localize in between the two layers. We find that disruption of SYCE2 and TEX12 (a fourth CE protein) localization to the CE abolishes central alignment of the N-terminal region of SYCP1. Thus, our results show that all four CE proteins in an interdependent manner contribute to stabilization of opposing N-terminal regions of SYCP1, forming a bilayered TF-CE junction structure that promotes SC formation and synapsis.