The nuclei were isolated from HeLa cells with nuclear extraction reagents (Thermo, NE-PER™) and suspended in 1 X PBS buffer (pH 7.4). The suspension of intact nuclei was crosslinked by adding 5 mM BSP (chemical structure shown in Figure S1, with the maximum Cα-Cα distance restraints of 28 Å ) every 20 min for 3 times at room temperature and quenched with 50 mM ammonium bicarbonate. To further improve the identification coverage of NRPC, the cross-linker of 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methyl morpholinium chloride (DMTMM) was used, combining with the amino-reactive BSP for the crosslinking of nuclear envelopes (NEs) isolated from HeLa cells with commercial kit (invent, NE-013™), respectively.