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Figure 3.
Fig. 3. Comparison of the x-ray and EM structures of EmrE-TPP.
(A) Independent superposition of EmrE subunits A and B in the
x-ray structure with a cylinder model (colored gray) derived
from the EM structure of EmrE-TPP (European Molecular Biology
Laboratory-EBI accession code EMD-1087) (13). A unique match was
found using two constraints: Three-helix bundles on opposite
sides of the dimer were assumed to be helices 1 to 3, and the
helix closest to the density attributed to TPP in the EM map was
assumed to be helix 1. In this pseudo-atomic model, three
helices have notably different tilt angles: A2, B2, and B3
(shown by red asterisks). The x-ray position of helices B2 and
B3, which appear to move as a unit, is likely due to crystal
packing interactions along the putative tetramerization
interface (see also Fig. 1E). We speculate that the
conformational change in helix A2 is relevant to the drug
transport mechanism. (B and C) The TPP molecule is bound to
different sites in the x-ray structure (C) and EM model (B),
suggesting a possible mechanism for drug transport. The relative
positions of the EmrE helices are indicated, viewing toward the
binding pockets (in the same orientation as in Fig. 1C). The
positions of the TPP molecules are shown by red circles.
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