Fig. 7: Mechanism of Rnf.

a Scheme of the ET pathway (highlighted as red lines). The electron flows from the reduced cytoplasmic Fd-like protein (dashed rectangle) modeled in contact with RnfB via RnfB and the membrane-spanning RnfAE to the extracellular RnfG and from there back via RnfD and RnfC to NAD⁺. The [4Fe-4S] clusters are shown as brown cubes and the flavins as yellow triplex-hexagons. The shortest distance between electron carriers of RnfB and RnfC is 25 Å (gray). b ET from [4Fe-4S]_RnfB-2 to Fe_RnfAE via Fe_RnfB-1. FdI (in surface representation) is drawn in green in the position found in the EM structure, in yellow in the position obtained from an Alphafold2 model of RnfB and in coral in the manually modeled position attached to RnfAE. The [4Fe-4S] cluster is shifted ca. 15 Å from the Alphafold2 to the modeled position. The C-terminal helix of RnfAE (dark blue) contacting FdI interacts with helix 126:136 (V) of RnfD (purple) that might be part of the cytoplasmic Na⁺ binding site (indicated by an arrow). c Scheme of the redox-driven Na⁺ transport. Na⁺ enter from the cytoplasmic side and binds in front of the locked channel (left panel). Upon channel opening (central panel) Na⁺ migrates to the extracellular half-channel (right panel), from where it is released after conformational change of the occlusion loop. FMN and FMN•⁻ are drawn in yellow and orange, RBFH• and RBFH₂ in salmon and violet, respectively. The presented scenario is based on conformational changes of helices VII, VIII, IX, and X induced by cytoplasmic Na⁺ binding, RnfG reorientation, low-potential FMN_RnfD semiquinone anion formation and accompanied conformational changes. Helices V and VII are omitted for clarity. A switch to turn redox-dependent on and off conformational changes for propagation to an effector site (Na⁺ channel) is a well-known phenomenon in biochemistry⁶².