Cryo-EM structure (2DX) of EDTA-treated YiiP from tubular crystals. (A) Density map at 4.2-Å resolution of an isolated YiiP dimer masked from 3-D reconstruction of tubular crystals from EDTA-treated WT YiiP. The previous structure from untreated tubular crystals (PDB accession no. 5VRF) is docked as a rigid body, illustrating the similarity in the conformation. Horizontal lines indicate the membrane boundary. (B) The previous structure (5VRF) derived from tubular crystals showing the overall architecture of the dimer and the location of the three Zn binding sites. Zn ions are shown as pink spheres. (C) Detailed view of Zn binding site A at which the map from EDTA-treated YiiP reveals strong density, indicating that a metal ion is bound at this site. (D) Detailed view of Zn binding site B showing an ordered loop between M2 and M3 and density associated with the metal ion and coordinating residues. Side chains do not perfectly match the density, because 5VRF was only fitted as a rigid body and was not explicitly refined to this map.