EMD-28881

Single-particle
3.8 Å
EMD-28881 Deposition: 16/11/2022
Map released: 08/02/2023
Last modified: 23/10/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-28881

Cryo-EM structure of a Zinc-loaded wild-type YiiP-Fab complex

EMD-28881

Single-particle
3.8 Å
EMD-28881 Deposition: 16/11/2022
Map released: 08/02/2023
Last modified: 23/10/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Shewanella oneidensis, Homo sapiens
Sample: Wild-type Zinc-loaded YiiP-Fab complex
Fitted models: 8f6e (Avg. Q-score: 0.412)

Deposition Authors: Lopez-Redondo ML , Hussein AK , Stokes DL
Energy coupling and stoichiometry of Zn 2+ /H + antiport by the prokaryotic cation diffusion facilitator YiiP.
PUBMED: 37906094
DOI: doi:10.7554/eLife.87167
ISSN: 2050-084X
Abstract:
YiiP from Shewanella oneidensis is a prokaryotic Zn2+/H+ antiporter that serves as a model for the Cation Diffusion Facilitator (CDF) superfamily, members of which are generally responsible for homeostasis of transition metal ions. Previous studies of YiiP as well as related CDF transporters have established a homodimeric architecture and the presence of three distinct Zn2+ binding sites named A, B, and C. In this study, we use cryo-EM, microscale thermophoresis and molecular dynamics simulations to address the structural and functional roles of individual sites as well as the interplay between Zn2+ binding and protonation. Structural studies indicate that site C in the cytoplasmic domain is primarily responsible for stabilizing the dimer and that site B at the cytoplasmic membrane surface controls the structural transition from an inward facing conformation to an occluded conformation. Binding data show that intramembrane site A, which is directly responsible for transport, has a dramatic pH dependence consistent with coupling to the proton motive force. A comprehensive thermodynamic model encompassing Zn2+ binding and protonation states of individual residues indicates a transport stoichiometry of 1 Zn2+ to 2-3 H+ depending on the external pH. This stoichiometry would be favorable in a physiological context, allowing the cell to use the proton gradient as well as the membrane potential to drive the export of Zn2+.