Extended Data Fig. 7: Crosslinking mass spectrometry of endogenous TREX–mRNPs.

a. Crosslinks mapped onto TREX monomers 1A and 1B. Monomer 1A and 1B are shown as transparent surfaces and crosslinks are colored according to the Cα-Cα distance of crosslinked residues. Symmetry related monomers 2A and 2B are shown in ribbon representation and colored as in Fig. 2d. Crosslinks that span more than 30 Å may be explained through proximity between TREX complexes on mRNPs, as observed in our cryo-ET data. The data was generated from two purification and crosslinking experiments, which were merged for data analysis (see methods). b. Crosslinks mapped onto the ALYREF–EJC–RNA protomer structure. c. Crosslinks mapped onto the ALYREF–EJC–RNA dimer structure are similarly compatible both with inter EJC-EJC (dimer) as well as with intra-EJC crosslink distances (protomer, panel b). Crosslinks spanning less than 30 Å are shown. d. The ALYREF–MAGOH crosslinks mapped onto a model generated by superposing the ALYREF AlphaFold model onto the ALYREF-RRM. ALYREF residues in the AlphaFold model that are absent from the ALYREF–EJC–RNA structure are shown as transparent ribbons. e. Histograms and pie charts of Cα-Cα distances of crosslinked residues in the TREX structure. f. As panel e, but for the ALYREF–EJC–RNA structure. g. Protein-protein interaction network based on crosslinks of TREX–mRNPs after a one-step purification without nuclease digestion. Note that ribosomal proteins are common contaminants. The thickness of the grey lines connecting proteins scales with the number of unique crosslinked residue pairs.