Cryo-EM based theoretical model structure of transmembrane domain of the multidrug-resistance antiporter from E. coli EmrE

Experimental Data Snapshot


wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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

Fleishman, S.J.Harrington, S.E.Enosh, A.Halperin, D.Tate, C.G.Ben-Tal, N.

(2006) J Mol Biol 364: 54-67

  • DOI: https://doi.org/10.1016/j.jmb.2006.08.072
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    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 Angstroms 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 C alpha 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.

  • Organizational Affiliation

    Department of Biochemistry, George S Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein emrE
A, B
137Escherichia coliMutation(s): 0 
Gene Names: emrEEBmvrC
Membrane Entity: Yes 
Find proteins for P23895 (Escherichia coli (strain K12))
Explore P23895 
Go to UniProtKB:  P23895
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23895
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 1α = 90
b = 1β = 90
c = 1γ = 90

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Author supporting evidence, Data collection, Database references