Figure 6. A structure-guided model of the conformational cycle and thermodynamic landscape of metal transport by Nramps.

(A) After Mn²⁺ enters through the outer vestibule between TM6a and TM10 in the outward-open state, a bulk conformation change closes the outer gate. The occluded conformation arises though rearrangements of TM6a and TM10 facilitated by formation of the T228 and Q378 networks, respectively. The inner gate partially opens in the occluded state as the R244 network breaks and TM5 moves. To achieve the inward-open conformation, disruption of the Q89 network frees TM1a to swing up to fully open the inner vestibule for Mn²⁺ release into the cytosol. (B) Our data indicate that the most stable Mn²⁺-bound state is the occluded state, and the three main states are readily accessible to facilitate transport. In contrast, Cd²⁺ binding stabilizes the inward-open state.

Figure 6—figure supplement 1. Comparison of coordination spheres of different Mn²⁺-binding proteins: MntR, a Mn²⁺ regulator (PDB ID: 1ON1) (Glasfeld et al., 2003); PsaA, the solute-binding protein domain of Mn²⁺-transporting ATP-binding cassette transporter (PDB ID: 3ZTT) (Couñago et al., 2014); and the DraNramp WT•Mn²⁺ occluded structure (this work).

In all structures, Mn²⁺ binds in an octahedral coordination. The geometry is more distorted (RMS_angle=25°) and bond distances are longer in DraNramp, perhaps to enable Mn²⁺ transport and the associated protein dynamics. In comparison, the geometry is close to ideal (RMS_angle=8°) and bond distances shorter in MntR, where Mn²⁺ binding, but not transport, is essential for regulating downstream signaling.