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Structure of a Na+/H+ antiporter and insights into mechanism of action and regulation by pH


The control by Na+/H+ antiporters of sodium/proton concentration and cell volume is crucial for the viability of all cells. Adaptation to high salinity and/or extreme pH in plants and bacteria or in human heart muscles requires the action of Na+/H+ antiporters. Their activity is tightly controlled by pH. Here we present the crystal structure of pH-downregulated NhaA, the main antiporter of Escherichia coli and many enterobacteria. A negatively charged ion funnel opens to the cytoplasm and ends in the middle of the membrane at the putative ion-binding site. There, a unique assembly of two pairs of short helices connected by crossed, extended chains creates a balanced electrostatic environment. We propose that the binding of charged substrates causes an electric imbalance, inducing movements, that permit a rapid alternating-access mechanism. This ion-exchange machinery is regulated by a conformational change elicited by a pH signal perceived at the entry to the cytoplasmic funnel.

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We acknowledge the beamtime and the assistance of the personnel at beamlines ID29 and ID23 at the European Synchrotron Facility and at PX06 at the Swiss Light Source. This study was supported by grants from the German Israeli Foundation for Scientific Research and Development (to H.M. and E.P.), the Max Planck Society, the Fonds der Chemischen Industrie and the Israel Science Foundation (to E.P.). E.S. was supported by the International Max Planck Research School (IMPResS).

Author information

Correspondence to Carola Hunte or Etana Padan or Hartmut Michel.

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Competing interests

Coordinates have been deposited in the Protein Data Bank under accession code 1ZCD. Reprints and permissions information is available at The authors declare no competing financial interests.

Supplementary information

Supplementary Methods

Over-expression, purification, crystallization of NhaA; data collection and structure determination. (DOC 40 kb)

Supplementary Table S1

Data collection and refinement statistics for NhaA structure determination. (DOC 33 kb)

Supplementary Figure S1

Organisation of the 12 TMSs of NhaA in two main helical bundles; periplasmic and cytoplasmic view. (PDF 1127 kb)

Supplementary Figure S2

Structural homology between TMS III, IV and V onto TMS X, XI, and XII of NhaA; stereo view of the superimposed elements. (PDF 966 kb)

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Further reading

Figure 1: Experimental electron density.
Figure 2: Overall architecture of NhaA.
Figure 3: Substrate passage and periplasmic barrier.
Figure 4: Structural basis of Na + /H + translocation and pH regulation.
Figure 5: Proposed mechanism of pH regulation and translocation of NhaA.


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