Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy

Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2140-5. doi: 10.1073/pnas.1215455110. Epub 2013 Jan 22.


YiiP is a dimeric Zn(2+)/H(+) antiporter from Escherichia coli belonging to the cation diffusion facilitator family. We used cryoelectron microscopy to determine a 13-Å resolution structure of a YiiP homolog from Shewanella oneidensis within a lipid bilayer in the absence of Zn(2+). Starting from the X-ray structure in the presence of Zn(2+), we used molecular dynamics flexible fitting to build a model consistent with our map. Comparison of the structures suggests a conformational change that involves pivoting of a transmembrane, four-helix bundle (M1, M2, M4, and M5) relative to the M3-M6 helix pair. Although accessibility of transport sites in the X-ray model indicates that it represents an outward-facing state, our model is consistent with an inward-facing state, suggesting that the conformational change is relevant to the alternating access mechanism for transport. Molecular dynamics simulation of YiiP in a lipid environment was used to address the feasibility of this conformational change. Association of the C-terminal domains is the same in both states, and we speculate that this association is responsible for stabilizing the dimer that, in turn, may coordinate the rearrangement of the transmembrane helices.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Bacterial Proteins / ultrastructure
  • Cation Transport Proteins / chemistry*
  • Cation Transport Proteins / genetics
  • Cation Transport Proteins / metabolism
  • Cation Transport Proteins / ultrastructure
  • Cryoelectron Microscopy
  • Crystallography, X-Ray
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Protein Conformation
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Recombinant Proteins / ultrastructure
  • Sequence Homology, Amino Acid
  • Shewanella / genetics
  • Shewanella / metabolism
  • Zinc / metabolism


  • Bacterial Proteins
  • Cation Transport Proteins
  • Recombinant Proteins
  • Zinc

Associated data

  • PDB/3J1Z
  • PDB/EMD-5450