Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

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.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

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.


  1. Padan,E. et al. The molecular mechanism of regulation of the NhaA Na+/H+ antiporter of Escherichia coli, a key transporter in the adaptation to Na+ and H+. Novartis Found. Symp. 221, 183–196 (1999).

    CAS  PubMed  Google Scholar 

  2. Padan,E. & Schuldiner,S. in Handbook of Biological Physics (eds Konings, W. N., Kaback, H. R. & Lolkema, J. S.) 501–531 (Elsevier, Oxford, 1996).

    Google Scholar 

  3. Rothman,A., Padan,E. & Schuldiner,S. Topological analysis of NhaA, a Na+/H+ antiporter from Escherichia coli. J. Biol. Chem. 271, 32288–32292 (1996).

    Article  CAS  Google Scholar 

  4. Williams,K. A. et al. Projection structure of NhaA, a secondary transporter from Escherichia coli, at 4.0?Å resolution. EMBO J. 18, 3558–3563 (1999).

    Article  CAS  Google Scholar 

  5. Blakely,R. D., De Felice,L. J. & Hartzell,H. C. Molecular physiology of norepinephrine and serotonin transporters. J. Exp. Biol. 196, 263–281 (1994).

    CAS  PubMed  Google Scholar 

  6. Schloss,P. & Williams,D. C. The serotonin transporter: a primary target for antidepressant drugs. J. Psychopharmacol. 12, 115–121 (1998).

    Article  CAS  Google Scholar 

  7. Wright,E. M. Glucose galactose malabsorption. Am. J. Physiol. 275, 879–882 (1998).

    Google Scholar 

  8. Saier,M. H. Jr et al. Evolutionary origins of multidrug and drug-specific efflux pumps in bacteria. FASEB J. 12, 265–274 (1998).

    Article  CAS  Google Scholar 

  9. Kaback,H. R. & Wu,J. From membrane to molecule to the third amino acid from the left with a membrane transport protein. Q. Rev. Biophys. 30, 333–364 (1997).

    Article  CAS  Google Scholar 

  10. Iwata,S., Ostermeier,C., Ludwig,B. & Michel,H. Structure at 2.8?Å resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 376, 660–669 (1995).

    Article  ADS  CAS  Google Scholar 

  11. Auer,M., Scarborough,G. A. & Kühlbrandt,W. Three-dimensional map of the plasma membrane H+-ATPase in the open conformation. Nature 392, 840–843 (1998).

    Article  ADS  CAS  Google Scholar 

  12. Zhang,P. et al. Structure of the calcium pump from sarcoplasmic reticulum at 8?Å resolution. Nature 392, 835–839 (1998).

    Article  ADS  CAS  Google Scholar 

  13. Henderson,R. et al. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J. Mol. Biol. 213, 899–929 (1990).

    Article  CAS  Google Scholar 

  14. Grigorieff,N., Ceska,T. A., Downing,K. H., Baldwin,J. M. & Henderson,R. Electron-crystallographic refinement of the structure of bacteriorhodopsin. J. Mol. Biol. 259, 393–421 (1996).

    Article  CAS  Google Scholar 

  15. Havelka,W. A., Henderson,R. & Oesterhelt,D. Three-dimensional structure of halorhodopsin at 7?Å resolution. J. Mol. Biol. 247, 726–738 (1995).

    CAS  PubMed  Google Scholar 

  16. Doyle,D. A. et al. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280, 69–77 (1998).

    Article  ADS  CAS  Google Scholar 

  17. Chang,G., Spencer,R. H., Lee,A. T., Barclay,M. T. & Rees,D. C. Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel. Science 282, 2220–2226 (1998).

    Article  ADS  CAS  Google Scholar 

  18. Walz,T. et al. The three-dimensional structure of aquaporin-1. Nature 387, 624–627 (1997).

    Article  ADS  CAS  Google Scholar 

  19. Cheng,A. et al. Three-dimensional organization of a human water channel. Nature 387, 627–630 (1997).

    Article  ADS  CAS  Google Scholar 

  20. Li,H., Lee,S. & Jap,B. K. Molecular design of aquaporin-1 water channel as revealed by electron crystallography. Nature Struct. Biol. 4, 263–265 (1997).

    Article  CAS  Google Scholar 

  21. Rothman,A., Gerchman,Y., Padan,E. & Schuldiner,S. Probing the conformation of NhaA, a Na+/H+ antiporter from Escherichia coli, with trypsin. Biochemistry 36, 14572–14576 (1997).

    Article  CAS  Google Scholar 

  22. Unwin,N. Acetylcholine receptor in the open state. Nature 373, 37–43 (1995).

    Article  ADS  CAS  Google Scholar 

  23. Subramaniam,S. et al. Protein conformational changes in the bacteriorhodopsin photocycle. J. Mol. Biol. 287, 145–161 (1999).

    Article  CAS  Google Scholar 

  24. Peruse,E., Courts,D. M. & Cull,L. G. Structural rearrangements underlying K+ channel activation gating. Science 285, 73–78 (1999).

    Article  Google Scholar 

  25. Wang,D. N. & Kühlbrandt,W. High-resolution electron crystallography of light-harvesting chlorophyll a/b-protein complex in three different media. J. Mol. Biol. 217, 691–699 (1991).

    Article  CAS  Google Scholar 

  26. Henderson,R. et al. Structure of purple membrane from Halobacterium halobium: recording, measurement and evaluation of electron micrographs at 3.5?Å resolution. Ultramicroscopy 19, 899–929 (1986).

    Article  Google Scholar 

  27. Crowther,R. A., Henderson,R. & Smith,J. M. MRC image processing programs. J. Struct. Biol. 116, 9–16 (1996).

    Article  CAS  Google Scholar 

  28. Shaw,P. J. & Hills,G. J. Tilted specimen in the electron microscope: a simple specimen holder and the calculation of tilt angles from crystalline specimens. Micron 12, 279–282 (1981).

    Google Scholar 

  29. Unger,V. M. & Schertler,G. F. X. Low resolution structure of bovine rhodopsin determined by electron cryo-microscopy. Biophys. J. 68, 1776–1786 (1995).

    Article  ADS  CAS  Google Scholar 

  30. Jones,T. A., Zou,J. Y., Cowan,S. W. & Kjeldgaard,M. Improved methods for building protein models in electron density maps. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

Download references


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.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Karen A. Williams.

Supplementary information

Supplementary Information

Supplementary Information (PDF 59 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing