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Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase

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Ion-translocating rotary ATPases serve either as ATP synthases, using energy from a transmembrane ion motive force to create the cell’s supply of ATP, or as transmembrane ion pumps that are powered by ATP hydrolysis1. The members of this family of enzymes each contain two rotary motors: one that couples ion translocation to rotation and one that couples rotation to ATP synthesis or hydrolysis. During ATP synthesis, ion translocation through the membrane-bound region of the complex causes rotation of a central rotor that drives conformational changes and ATP synthesis in the catalytic region of the complex. There are no structural models available for the intact membrane region of any ion-translocating rotary ATPase. Here we present a 9.7 Å resolution map of the H+-driven ATP synthase from Thermus thermophilus obtained by electron cryomicroscopy of single particles in ice. The 600-kilodalton complex has an overall subunit composition of A3B3CDE2FG2IL12. The membrane-bound motor consists of a ring of L subunits and the carboxy-terminal region of subunit I, which are equivalent to the c and a subunits of most other rotary ATPases, respectively. The map shows that the ring contains 12 L subunits2 and that the I subunit has eight transmembrane helices3. The L12 ring and I subunit have a surprisingly small contact area in the middle of the membrane, with helices from the I subunit making contacts with two different L subunits. The transmembrane helices of subunit I form bundles that could serve as half-channels across the membrane, with the first half-channel conducting protons from the periplasm to the L12 ring and the second half-channel conducting protons from the L12 ring to the cytoplasm. This structure therefore suggests the mechanism by which a transmembrane proton motive force is converted to rotation in rotary ATPases.

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Figure 1: Three-dimensional map of the T. thermophilus ATP synthase.
Figure 2: Fitting of the C subunit crystal structure.
Figure 3: The membrane-bound region of the enzyme.
Figure 4: Model for proton translocation.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The cryo-EM map of the T. thermophilus H+-driven ATP synthase is deposited in Electron Microscopy Data Bank under accession code EMD-5335; the docked atomic models are deposited in Protein Data Bank under accession number 3J0J.

Change history

  • 11 January 2012

    The placement of an arrow was corrected in Fig. 4b.


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We thank V. Kanelis, F. Sicheri, P. Rosenthal, L. Kay and R. Henderson for discussions and reading this manuscript, and J. Walker and R. Pomès for discussions. Computations were performed on the general-purpose cluster supercomputer at the SciNet HPC Consortium. W.C.Y.L. was supported by an Ontario Graduate Scholarship. J.L.R. was supported by a New Investigator Award from the Canadian Institutes of Health Research and an Early Researcher Award from the Ontario Ministry of Research and Innovation. This research was funded by operating grant MOP 81294 from the Canadian Institutes of Health Research.

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Authors and Affiliations



J.L.R. and W.C.Y.L. designed the experiments and J.L.R. supervised the research. W.C.Y.L. performed protein purification and cryo-EM. J.L.R. wrote new computer programs. W.C.Y.L. and J.L.R. performed the image analysis, interpreted the data and wrote the manuscript.

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Correspondence to John L. Rubinstein.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Figures 1-4 with legends, Supplementary Table 1 and additional references. (PDF 1639 kb)

Supplementary Movie 1

The movie shows a 3-D map with docked crystals structures of subunits A (yellow), B (red), C (cyan), D (blue), E (purple), F (orange), and G (beige) subunits and segments for density from subunits I (green), L (magenta), and the missing density from subunit D (blue). The scale bar corresponds to 25 Å . (MOV 20549 kb)

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Lau, W., Rubinstein, J. Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase. Nature 481, 214–218 (2012).

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