X-ray structure of EmrE supports dual topology model

Chen et al. 10.1073/pnas.0709387104.

Supporting Information

Files in this Data Supplement:

SI Figure 5
SI Table 2
SI Figure 6
SI Figure 7
SI Movie 1
SI Movie 2
SI Figure 8
SI Movie 3
SI Figure 9

Fig. 5. View of the apo EmrE dimer, showing anomalous Fourier density (4s) derived from mercury-derivatized proteins, with wild type colored in red and C41S in white. The protein backbones are shown in Ca trace, with one monomer colored in blue and the other in green. The Hg markers establish the positions of the indicated cysteine residues.

Fig. 6. View of the P2₁ asymmetric unit of EmrE-TPP, which contains two dimers related by a noncrystallographic twofold axis. The dimer on the left shows the front monomer rendered in a color gradient, from green at the N terminus to yellow at the C terminus, and the back monomer is in gray. In the dimer on the right, the monomer colored in blue is equivalent to the back monomer of the left dimer, whereas the monomer colored in gray is equivalent to the front monomer in the left. The a and b unit cell coordinate axes are indicated.

Fig. 7. Views of aromatic side chains with corresponding densities. The TPP molecule is colored red.

Fig. 8. Stereoview of the TPP-bound EmrE monomers, superimposed via the first three TM helices. The relative positions of TM1-3, but not TM4, are structurally more conserved between the two monomers.

Fig. 9. (A) Superposition of the x-ray structure with the computational model by Fleishman et al. (22). (B) Side-by-side comparison of the x-ray structure (Left) and the computational model (Right). Selected residues are shown as spheres and labeled, to facilitate comparison of the relative rotational orientations of the helices.

SI Movie 1

Movie 1. SIGMAA-weighted 2F_o - F_c composite omit map (1s) calculated by using a maximum likelihood refinement target (mlf) for EmrE-TPP (C2 form). The asymmetric unit contains one dimer. The color scheme is the same as in Fig. 2. Anomalous Se density are shown in red (3s), and As is in magenta (4s).

SI Movie 2

Movie 2. SIGMAA-weighted 2F_o - F_c composite omit map (1s) calculated by using a maximum likelihood refinement target (mlf) for EmrE-TPP (P2₁ form). The asymmetric unit contains two dimers. The color scheme is the same as in Fig. 2. Anomalous Se density is shown in red (3s).

SI Movie 3

Movie 3. Ribbon representation of the EmrE-TPP x-ray structure docked into the EM density map (14), contoured at 1.4s. The x-ray model is colored by using the same scheme as in Fig. 3.

Table 2. Structure statistics

^† Data from retracted manuscripts.

^‡ Only data from experimental map calculation were used to maximize the accuracy of the model.

^§ C41S mutant x-ray data.

^¶ R_sym = S|I - <I>|/S|<I>|, where I is the measured intensity of each reflection, and <I> is the intensity averaged from symmetry equivalents.

^║ R_cryst = S|F_o - F_c|/S|F_c|, where F_o and F_c are observed and calculated structure factors, respectively.

^†† R_free was calculated from a test set (8-10%) omitted from the refinement.

^‡‡ The values reflect anisotropy in the diffraction data.

^§§ Root mean square deviation.

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