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. 2017 Jul 26;45(17):9976–9989. doi: 10.1093/nar/gkx656

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© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 4. — Structural comparison of STM1697–stFlhD and YdiV–mgFlhD. (A) Structural superposition of STM1697 and YdiV. The two structures are shown in cartoon mode (YdiV: light yellow, STM1697: green). The FlhD binding sites for STM1697 and YdiV are indicated by circles. (B) Structural superposition of STM1697–stFlhD and YdiV–FlhD. The stFlhD in the STM1697–stFlhD structure is used as the reference structure and YdiV-FlhD is superimposed onto the STM1697–stFlhD complex (stFlhD: blue, mgFlhD: light blue, YdiV: light yellow, STM1697: green). (C) Details of changes in the stFlhD and mgFlhD (stFlhD from Salmonella typhimurium, mgFlhD from Escherichia coli MG1655) in the complex structure. Residues located in the interface are shown in stick mode with different colors (stFlhD: hotpink, mgFlhD: blue). The positional changes of the side-chains of 14Y and 26R are indicated by arrows. (D) The structure of FlhD₄C₂ is used as a model, and STM1697–stFlhD and YdiV–FlhD are separately superimposed onto the third FlhD molecule of FlhD₄C₂ (STM1697: orange, YdiV: yellow, FlhD: blue). Whole structures are shown in cartoon mode. The right figure presents a close-up view of the interface between the second and the third FlhD molecules of FlhD₄C₂. All interfaces are overlapped, and the interface of YdiV–FlhD shows more interactions than STM1697–stFlhD and D2–D3. (E) STM1697 and FlhD₄C₂ cannot form the (STM1697)₄ FlhD₄C₂ hetero-decamer. Size-exclusion chromatography (SEC) results of the 2:1 and 5:1 mixtures of STM1697 and FlhD₄C₂. The STM1344 and FlhD₄C₂ mixture is used as a positive control because it forms the (STM1344)₄ FlhD₄C₂ hetero-decamer in vitro. FlhD₄C₂ alone is used as another control. The elution volume of every peak value is marked in the corresponding colors. STM1697₂FlhD₄C₂ complex appeared in solution, but no hetero-decamer formed when the ratio of STM1697 and FlhD₄C₂ reached 5:1. The right figure presents the model of the STM1697₂FlhD₄C₂ hetero-hexamer.