7KZX

Cryo-EM structure of YiiP-Fab complex in Apo state

Summary for 7KZX

• Entry DOI: 10.2210/pdb7kzx/pdb
• EMDB information: 23092
• Descriptor: Cadmium and zinc efflux pump FieF, Fab2R light chain, Fab2R heavy chain (3 entities in total)
• Functional Keywords: zinc, transporter, cation diffusion facilitator, holo state, inward-facing state, membrane protein
• Biological source: Shewanella oneidensis; More
• Total number of polymer chains: 6
• Total formula weight: 162943.61

Authors

Lopez-Redondo, M.L.,Fan, S.,Koide, A.,Koide, S.,Beckstein, O.,Stokes, D.L. (deposition date: 2020-12-10, release date: 2021-01-06, Last modification date: 2024-11-06)

Primary citation

Lopez-Redondo, M.,Fan, S.,Koide, A.,Koide, S.,Beckstein, O.,Stokes, D.L.
Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP.
J.Gen.Physiol., 153:-, 2021

PubMed Abstract: YiiP is a secondary transporter that couples Zn2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn2+. To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn2+ and validated its performance with known Zn2+-binding proteins. Using these tools, we find that, in the presence of Zn2+, YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn2+ binding sites and their role in the conformational dynamics that govern the transport cycle.

PubMed: 34254979
DOI: 10.1085/jgp.202112873

Experimental method

ELECTRON MICROSCOPY (4 Å)