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Three-dimensional structure of the ion-coupled transport protein NhaA


Ion-coupled membrane-transport proteins, or secondary transporters, comprise a diverse and abundant group of membrane proteins that are found in all organisms. These proteins facilitate solute accumulation and toxin removal against concentration gradients using energy supplied by ion gradients across membranes. NhaA is a Na+/H+ antiporter of relative molecular mass 42,000, which is found in the inner membrane of Escherichia coli, and which has been cloned and characterized1,2. NhaA uses the H+ electrochemical gradient to expel Na+ from the cytoplasm, and functions primarily in the adaptation to high salinity at alkaline pH1,2. Most secondary transporters, including NhaA3, are predicted to have 12 transmembrane helices. Here we report the structure of NhaA, at 7?Å resolution in the membrane plane and at 14?Å vertical resolution, determined from two-dimensional crystals4 using electron cryo-microscopy. The three-dimensional map of NhaA reveals 12 tilted, bilayer-spanning helices. A roughly linear arrangement of six helices is adjacent to a compact bundle of six helices, with the density for one helix in the bundle not continuous through the membrane. The molecular organization of NhaA represents a new membrane-protein structural motif and offers the first insights into the architecture of an ion-coupled transport protein.

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Figure 1: The 3D map of NhaA at 7?Å resolution viewed normal to the membrane plane.
Figure 2: Horizontal slices through the NhaA dimer.
Figure 3: Vertical sections through the NhaA 3D map.
Figure 4: Overview of the interactions between adjacent dimers of NhaA.


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I thank W. Kühlbrandt for his support and encouragement throughout this project, D. Mills for assistance with the JEOL 3000 SFF, V. Unger for advice on image processing, U. Geldmacher-Kaufer for technical assistance, and S. Schuldiner, E. Padan and A. Rothman for their assistance with NhaA biochemistry during the early stages of this work. This work was supported by the Deutsche Forschungsgesellshaft.

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Correspondence to Karen A. Williams.

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Williams, K. Three-dimensional structure of the ion-coupled transport protein NhaA. Nature 403, 112–115 (2000).

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