Role of membrane-proximal rim domain in facilitating pore formation by VCC . (A) Cryo-EM 3D reconstruction of liposome-bound VCC resolved at 4 Å. Protein is colored blue, and the lipid density is rendered transparent. (B) A transparent representation of density map fitted with the atomic model of VCC. Enlarged view shows the extent of immersion of the membrane-proximal portion of the atomic model within the lipid layer. (C) Two adjacent monomers of the atomic model visualized within the cryo-EM map at a high threshold of volume where lipid moieties are not observed. (D) A low threshold of volume shows the lipid densities intermingled with the side chains of the membrane-proximal rim domains. (E) Enlarged view of the cytolysin domain and the membrane-proximal rim shows amino acid residues observed to interact with the lipid moieties. (F) The distance between Leu361 and Val363 indicates that the rim domain is inserted by an additional 8 Å in near-physiological conditions.