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YiiP is a dimeric Zn2+/H+ antiporter from Eacherichia coil belonging to the cation diffusion facilitator family. We used cryoelectron microscopy to determine a 13-Å resolution structure of a YiiP homolog from Shewaneiia oneidensis within a lipid bilayer in the absence of Zn2+ Starting from the X-ray structure in the presence of Zn2+, we used molecular dynamics flexible fitting to build a model consistent with our map. Comparison of the structures suggests a conforma- tional change that involves pivoting of a transmembrane, four-helix bundle (M1, M2, M4, and M5) relative to the M3-M6 helix pair. Although accessibility of transport sites in the X-ray model indicates that it represents an outward-facing state, our model is consistent with an inward-facing state, suggesting that the conformational change is relevant to the alternating access mechanism for transport. Molecular dynamics simulation of YiiP in a lipid environment was used to address the feasibility of this conformational change. Association of the C-terminal domains is the same in both states, and we speculate that this association is responsible for stabilizing the dimer that in turn. may coordinate the rearrangement of the trans- membrane helices. [ABSTRACT FROM AUTHOR]