Fig. 3: Conformational landscape of heme binding and translocation.

a, Close-up views of residues involved in heme binding and occlusion. Surface model cross sections and side views illustrate the changing shape and size of the internal cavity and the TMH region in different conformational states. Heme is shown as purple ball-and-stick model. EL^D and TM4^D are shown as tubes. b, On heme entry and coordination, the membrane-embedded segment of TM4^D moves toward EL^D and thus closes the lateral gate of CydDC. c, The top shows the close-up view of the heme-binding site in the \({{{\mathrm{IF}}}}_{{{{\mathrm{confined}}}}}^{{{{\mathrm{heme}}}}}\) state. The bottom shows the sequence alignments of CydD and CydC heme binding-site forming regions of representative and disease related bacteria. Conserved residues are highlighted in magenta. Conserved amino acid groups are highlighted in gray. d, The top shows the changing EL^D–TM4^D distance during the transition from \({{{\mathrm{IF}}}}_{{{{\mathrm{asym}}}}}^{{{{\mathrm{apo}}}}}\) to \({{{\mathrm{IF}}}}_{{{{\mathrm{confined}}}}}^{{{{\mathrm{heme}}}}}\) states. The bottom shows a close-up view of the heme entry site in \({{{\mathrm{IF}}}}_{{{{\mathrm{bound}}}}}^{{{{\mathrm{heme}}}}}\) (beige) and \({{{\mathrm{IF}}}}_{{{{\mathrm{confined}}}}}^{{{{\mathrm{heme}}}}}\) (magenta) states, respectively. EL, elbow helix; IF, inward-facing; Occ, occluded; asym, asymmetrical.