PDBsum entry 3b5d

Membrane protein

PDB id: 3b5d

Contents

Protein chains

100 a.a.*

Ligands

P4P

* C-alpha coords only

References listed in PDB file

Key reference

Title

X-Ray structure of emre supports dual topology model.

Authors

Y.J.Chen, O.Pornillos, S.Lieu, C.Ma, A.P.Chen, G.Chang.

Ref.

Proc Natl Acad Sci U S A, 2007, 104, 18999-19004. [DOI no: 10.1073/pnas.0709387104]

PubMed id

18024586

Abstract

EmrE, a multidrug transporter from Escherichia coli, functions as a homodimer of a small four-transmembrane protein. The membrane insertion topology of the two monomers is controversial. Although the EmrE protein was reported to have a unique orientation in the membrane, models based on electron microscopy and now defunct x-ray structures, as well as recent biochemical studies, posit an antiparallel dimer. We have now reanalyzed our x-ray data on EmrE. The corrected structures in complex with a transport substrate are highly similar to the electron microscopy structure. The first three transmembrane helices from each monomer surround the substrate binding chamber, whereas the fourth helices participate only in dimer formation. Selenomethionine markers clearly indicate an antiparallel orientation for the monomers, supporting a "dual topology" model.

Figure 2.
Fig. 2. Structure determination of EmrE. (A) Experimental density for one apo EmrE monomer at 4.5-Å resolution. Anomalous Hg density (4 ), marking the positions of cysteine residues, is shown in red. The protein is shown in C^ trace and rendered in a color gradient, from green at the N terminus to yellow at the C terminus. (B) Ribbon representation of the distorted apo EmrE dimer. One monomer is rendered in color gradient with the helices labeled, and the other monomer is shown in gray. The approximate dimensions of a lipid bilayer are shown by the gray shading. (C) Views of the two apo EmrE monomers, with TM helices labeled. Note the extended configuration of the TM4 helices, which project away from the main body of the dimer. (D) Experimental density for one monomer of the EmrE-TPP complex at 3.8 Å (C2 crystal form), contoured at 1 . Anomalous Se density (3 ) is shown in red. (E) Side view of the EmrE-TPP dimer (C2 form), with the dimensions of the lipid bilayer indicated. One monomer is colored in gradient and labeled, and the other is in gray. The bound TPP is colored red. Density for the colored monomer terminates at residue 105. (F) Views of the two monomers (P2[1] form), which are essentially the same as the C2 monomers, except for the shorter TM helices, which terminate at the indicated residues. Full-length EmrE has 110 amino acid residues. Note that the superhelical twists of TM1–3 are similar in the apo and TPP-bound forms but that the helix packing interactions and monomer–monomer interactions differ.

Figure 3.
Fig. 3. EmrE binds TPP as an antiparallel dimer. (A) Stereoview of the EmrE transporter in complex with TPP. The two monomers are colored blue and yellow, and the bound TPP is pink. Anomalous Fourier density from SeMet (colored red in one monomer and green in the other) and the arsonium analogue of TPP (magenta) are shown contoured at 3 and 3.5 , respectively. The TPP and SeMet residue positions are labeled, with the two monomers distinguished by asterisks. (B) "Front" view of the transporter, emphasizing the positions of SeMet markers in TM1. The N termini of the monomers are labeled. (C) "Top" view of the EmrE-TPP structure, with the TM helices labeled. Red spheres indicate the positions of residues that have been implicated in substrate binding and transport by biochemical and mutagenesis studies (18, 20, 23–28). The only residue removed from the binding chamber is Leu-93 (TM4). In the x-ray crystals, this residue appears to mediate lattice interactions across a twofold symmetry axis relating two dimers. This crystal packing interface was also observed in the two-dimensional crystals used to derive the EM structure of EmrE-TPP (14).