AlphaFold2 predictions and MD simulations of the yeast SPC with and without Spc2. (A) Structural alignment of the AF2-predicted yeast SPC with the cryo-EM human SPC (Liaci et al., 2021). Spc2 in green, Sec11 in purple, Spc3 in red, Spc1 in orange. (B) Representative snapshot of the TM window membrane thickness for SPC with (top, WT) and without Spc2 (bottom, spc2Δ). The phosphate headgroups are colored in salmon (WT) or yellow (spc2Δ), and the lipid tails are represented as a transparent grey surface. (C) Model peptide illustrating that the difference in membrane thickness qualitatively fits with a hypothetical SPC substrate selectivity filter for SAs and SPs. (D) Membrane thickness computed for the ER membrane-embedded SPC using different protein models: a rigid model, elastic network models; a semi-flexible and fully flexible model. (E) Membrane thickness computed for a system composed of the yeast SPC embedded into a POPC membrane at atomistic or Martini 3 resolution.