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. 2019 Jun 27;8:e48385. doi: 10.7554/eLife.48385

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© 2019, Jamshad et al

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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Figure 5. — (A) X-ray crystal structure of SecAΔMBD at 3.5 Å solved by molecular replacement. The main body of the catalytic core in the asymmetric unit (Protomer 1) is coloured orange with the PPXD highlighted in cyan. The crystallographic mate (Protomer 2) interacts with promoter one using an interface similar to that found in 2FSG (Papanikolau et al., 2007), suggesting that this is the dimer interface of the purified protein in solution. The position of the most C-terminal residue that could be resolved (proline 834) is noted with an asterisk in the right panel. (B–E) Overlay of 10 independent structural models of SecA (B, C), SecAΔMBD (D) and SecAΔCTT (E) generated from fitting to the SAXS data using CORAL. The main body of the catalytic core is coloured grey, and the flexible residues are not displayed. (B, D, E) To facilitate visualization of the asymmetry in the in the dimeric models, both protomeric partners of the dimer were overlaid and the PPXD was coloured (blue/magenta) according to the protomer. The MBD is not displayed in panel B. (C) To facilitate visualization of the position of the MBD in the full-length protein, both protomeric partners of the dimer were overlaid and the MBD of the dimer pair that was located nearest to position 596 of the depicted protomer (orange) was displayed. In panel C, the PPXDs of two protomers, which occupy the same space as the MBDs, are not displayed. (F) Plot of the position of the PPXD in partners of the SecA dimer predicted by structural modelling. The distance between the α-carbon of amino acid 314, which is located near the centroid of the PPXD, and amino acid 596 in NBD2 was determined for each protomer and plotted against the distance in the second protomer. SecA, black circles (FL); SecAΔMBD, orange triangles (ΔMBD); SecAΔCTT, blue squares (ΔCTT). The grey diagonal line indicates the position of the distances if the dimers were symmetric. χ² values to the diagonal were calculated and used to determine p-values to test whether the asymmetry in the dimer was statistically significant.

Figure 5—figure supplement 1. — (A) X-ray crystal structure of SecAΔMBD at 3.5 Å solved by molecular replacement. The main body of the catalytic core in the asymmetric unit (Protomer 1) is coloured orange with the PPXD highlighted in cyan. The crystallographic mate (Protomer 2) interacts with promoter one using an interface similar to that found in 2FSG (Papanikolau et al., 2007), suggesting that this is the dimer interface of the purified protein in solution. The position of the most C-terminal residue that could be resolved (proline 834) is noted with an asterisk in the right panel. (B–E) Overlay of 10 independent structural models of SecA (B, C), SecAΔMBD (D) and SecAΔCTT (E) generated from fitting to the SAXS data using CORAL. The main body of the catalytic core is coloured grey, and the flexible residues are not displayed. (B, D, E) To facilitate visualization of the asymmetry in the in the dimeric models, both protomeric partners of the dimer were overlaid and the PPXD was coloured (blue/magenta) according to the protomer. The MBD is not displayed in panel B. (C) To facilitate visualization of the position of the MBD in the full-length protein, both protomeric partners of the dimer were overlaid and the MBD of the dimer pair that was located nearest to position 596 of the depicted protomer (orange) was displayed. In panel C, the PPXDs of two protomers, which occupy the same space as the MBDs, are not displayed. (F) Plot of the position of the PPXD in partners of the SecA dimer predicted by structural modelling. The distance between the α-carbon of amino acid 314, which is located near the centroid of the PPXD, and amino acid 596 in NBD2 was determined for each protomer and plotted against the distance in the second protomer. SecA, black circles (FL); SecAΔMBD, orange triangles (ΔMBD); SecAΔCTT, blue squares (ΔCTT). The grey diagonal line indicates the position of the distances if the dimers were symmetric. χ² values to the diagonal were calculated and used to determine p-values to test whether the asymmetry in the dimer was statistically significant.