title: Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy.
abstract: 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.
authors: Laboratory of Cryo-Electron Microscopy, New York Structural Biology Center, New York, NY 10027, USA.
authors: Nicolas
authors: N
authors: Coudray
authors: Salvatore
authors: S
authors: Valvo
authors: Minghui
authors: M
authors: Hu
authors: Ralph
authors: R
authors: Lasala
authors: Changki
authors: C
authors: Kim
authors: Martin
authors: M
authors: Vink
authors: Ming
authors: M
authors: Zhou
authors: Davide
authors: D
authors: Provasi
authors: Marta
authors: M
authors: Filizola
authors: Juoehi
authors: J
authors: Tao
authors: Jia
authors: J
authors: Fang
authors: Pawel A
authors: PA
authors: Penczek
authors: Iban
authors: I
authors: Ubarretxena-Belandia
authors: David L
authors: DL
authors: Stokes
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D027682:Cation Transport Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D020285:Cryoelectron Microscopy; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D017386:Sequence Homology, Amino Acid; D020592:Shewanella / Q000235:genetics / Q000378:metabolism; D015032:Zinc / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D027682:Cation Transport Proteins; D011994:Recombinant Proteins; D015032:Zinc