Visualization of cross-links on the TREX complex. (A) SDS–PAGE of the purified endogenous S. cerevisiae TREX complex. Subunits corresponding to Tho2, Hpr1-FLAG, Hrb1, Sub2, Mft1, Gbp2, Tex1, Thp2, and Yra1 were identified by mass spectrometry and are indicated accordingly. The asterisks indicate degradation bands. Molecular weight marker bands are indicated in kDa. (B) Scheme of the domain structures of TREX subunits. Flexible domains that are not observed in the solved structures are depicted in a lighter color. (C–E) Cross-links connecting residues within the same protein (C) and cross-links connecting residues of two different proteins (D) mapped on the sequence graphs of the corresponding proteins as black arcs and black lines, respectively. Segments longer than 25 residues that are missing in the PDB ID: 7apx structural model are shown as red lines on the sequence graph. Visualization was performed using xiNET (Combe et al. 2015). (C) Cross-linking data from this work. Cross-links that unambiguously correspond to intermolecular contacts between two molecules of the same protein are shown in blue as downward-facing loops. (D) Cross-links identified in this work. (E) Cross-links identified by Xie et al. (2021).
