F-box proteins lose their rigid-scaffold image: cryo-EM, cross-linking and deep learning show FBXL2's substrate domain swinging 43 Å
F-box proteins are the substrate-recruiting modules of SCF ubiquitin ligases and have long been treated as relatively rigid structural adaptors. This work combines cryo-EM structures, cross-linking mass spectrometry distance restraints and deep-learning conformational ensemble prediction to compare the same proteins across different complexes. FBXL2's substrate-binding domain moves 43 Å relative to its anchor domain, FBXL17 differs by 17 to 33 Å across assembly contexts, and FBXL1 shifts only 4.5 Å; FBXL2 needs at least four states to satisfy its cross-links to CSN.