5VRF

CryoEM Structure of the Zinc Transporter YiiP from helical crystals

Summary for 5VRF

• Entry DOI: 10.2210/pdb5vrf/pdb
• EMDB information: 8728
• Descriptor: Cadmium and zinc efflux pump FieF, ZINC ION (2 entities in total)
• Functional Keywords: zinc antiporter, membrane protein, cation diffusion facilitator, metal transport, helical crystals, structural genomics, psi-biology, transcontinental em initiative for membrane protein structure, temimps
• Biological source: Shewanella oneidensis MR-1
• Total number of polymer chains: 2
• Total formula weight: 65493.69

Authors

Coudray, N.,Lopez-Redondo, M.,Zhang, Z.,Alexopoulos, J.,Stokes, D.L.,Transcontinental EM Initiative for Membrane Protein Structure (TEMIMPS) (deposition date: 2017-05-10, release date: 2018-03-14, Last modification date: 2024-03-13)

Primary citation

Lopez-Redondo, M.L.,Coudray, N.,Zhang, Z.,Alexopoulos, J.,Stokes, D.L.
Structural basis for the alternating access mechanism of the cation diffusion facilitator YiiP.
Proc. Natl. Acad. Sci. U.S.A., 115:3042-3047, 2018

PubMed Abstract: YiiP is a dimeric antiporter from the cation diffusion facilitator family that uses the proton motive force to transport Zn across bacterial membranes. Previous work defined the atomic structure of an outward-facing conformation, the location of several Zn binding sites, and hydrophobic residues that appear to control access to the transport sites from the cytoplasm. A low-resolution cryo-EM structure revealed changes within the membrane domain that were associated with the alternating access mechanism for transport. In the current work, the resolution of this cryo-EM structure has been extended to 4.1 Å. Comparison with the X-ray structure defines the differences between inward-facing and outward-facing conformations at an atomic level. These differences include rocking and twisting of a four-helix bundle that harbors the Zn transport site and controls its accessibility within each monomer. As previously noted, membrane domains are closely associated in the dimeric structure from cryo-EM but dramatically splayed apart in the X-ray structure. Cysteine crosslinking was used to constrain these membrane domains and to show that this large-scale splaying was not necessary for transport activity. Furthermore, dimer stability was not compromised by mutagenesis of elements in the cytoplasmic domain, suggesting that the extensive interface between membrane domains is a strong determinant of dimerization. As with other secondary transporters, this interface could provide a stable scaffold for movements of the four-helix bundle that confers alternating access of these ions to opposite sides of the membrane.

PubMed: 29507252
DOI: 10.1073/pnas.1715051115

Experimental method

ELECTRON MICROSCOPY (4.1 Å)