Quasi-symmetry in the Cryo-EM Structure of EmrE Provides the Key to Modeling its Transmembrane Domain

Sarel J. Fleishman, Susan E. Harrington, Angela Enosh, Dan Halperin, Christopher G. Tate, Nir Ben-Tal*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

100 Scopus citations


Small multidrug resistance (SMR) transporters contribute to bacterial resistance by coupling the efflux of a wide range of toxic aromatic cations, some of which are commonly used as antibiotics and antiseptics, to proton influx. EmrE is a prototypical small multidrug resistance transporter comprising four transmembrane segments (M1-M4) that forms dimers. It was suggested recently that EmrE molecules in the dimer have different topologies, i.e. monomers have opposite orientations with respect to the membrane plane. A 3-D structure of EmrE acquired by electron cryo-microscopy (cryo-EM) at 7.5 Å resolution in the membrane plane showed that parts of the structure are related by quasi-symmetry. We used this symmetry relationship, combined with sequence conservation data, to assign the transmembrane segments in EmrE to the densities seen in the cryo-EM structure. A Cα model of the transmembrane region was constructed by considering the evolutionary conservation pattern of each helix. The model is validated by much of the biochemical data on EmrE with most of the positions that were identified as affecting substrate translocation being located around the substrate-binding cavity. A suggested mechanism for proton-coupled substrate translocation in small multidrug resistance antiporters provides a mechanistic rationale to the experimentally observed inverted topology.

Original languageEnglish
Pages (from-to)54-67
Number of pages14
JournalJournal of Molecular Biology
Issue number1
StatePublished - 17 Nov 2006


FundersFunder number
Clore Israel FoundationIST-006413
Hermann Minkowski-Minerva Center for Geometry at Tel-Aviv University
Israel Science Foundation


    • cryo-EM
    • dual topology
    • mechanism of action
    • protein structure prediction
    • structural bioinformatics


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