Cryo-EM structures provide insight into how E. coli F1Fo ATP synthase accommodates symmetry mismatch
Abstract
F1Fo ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a peripheral stalk. Proton flow through the Fo motor generates rotation of the central stalk, inducing conformational changes in the F1 motor that catalyzes ATP production. Here we present nine cryo-EM structures of E. coli ATP synthase to 3.1–3.4 Å resolution, in four discrete rotational sub-states, which provide a comprehensive structural model for this widely studied bacterial molecular machine. We observe torsional flexing of the entire complex and a rotational sub-step of Fo associated with long-range conformational changes that indicates how this flexibility accommodates the mismatch between the 3- and 10-fold symmetries of the F1 and Fo motors. We also identify density likely corresponding to lipid molecules that may contribute to the rotor/stator interaction within the Fo motor.
- Authors:
-
- The Victor Chang Cardiac Research Inst., Darlinghurst, NSW (Australia). Molecular, Structural and Computational Biology Division; Univ. of New South Wales, Sydney, NSW (Australia). St Vincent’s Clinical School. Faculty of Medicine
- The Victor Chang Cardiac Research Inst., Darlinghurst, NSW (Australia). Molecular, Structural and Computational Biology Division
- Univ. of Oxford (United Kingdom). Dept. of Chemistry
- Univ. of Oxford (United Kingdom). Clarendon Lab.
- The Victor Chang Cardiac Research Inst., Darlinghurst, NSW (Australia). Molecular, Structural and Computational Biology Division; Univ. of New South Wales, Sydney, NSW (Australia). St Vincent’s Clinical School. Faculty of Medicine
- Publication Date:
- Research Org.:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division
- OSTI Identifier:
- 1816612
- Grant/Contract Number:
- AC05-76RL01830
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Sobti, Meghna, Walshe, James L., Wu, Di, Ishmukhametov, Robert, Zeng, Yi C., Robinson, Carol V., Berry, Richard M., and Stewart, Alastair G. Cryo-EM structures provide insight into how E. coli F1Fo ATP synthase accommodates symmetry mismatch. United States: N. p., 2020.
Web. doi:10.1038/s41467-020-16387-2.
Sobti, Meghna, Walshe, James L., Wu, Di, Ishmukhametov, Robert, Zeng, Yi C., Robinson, Carol V., Berry, Richard M., & Stewart, Alastair G. Cryo-EM structures provide insight into how E. coli F1Fo ATP synthase accommodates symmetry mismatch. United States. https://doi.org/10.1038/s41467-020-16387-2
Sobti, Meghna, Walshe, James L., Wu, Di, Ishmukhametov, Robert, Zeng, Yi C., Robinson, Carol V., Berry, Richard M., and Stewart, Alastair G. Tue .
"Cryo-EM structures provide insight into how E. coli F1Fo ATP synthase accommodates symmetry mismatch". United States. https://doi.org/10.1038/s41467-020-16387-2. https://www.osti.gov/servlets/purl/1816612.
@article{osti_1816612,
title = {Cryo-EM structures provide insight into how E. coli F1Fo ATP synthase accommodates symmetry mismatch},
author = {Sobti, Meghna and Walshe, James L. and Wu, Di and Ishmukhametov, Robert and Zeng, Yi C. and Robinson, Carol V. and Berry, Richard M. and Stewart, Alastair G.},
abstractNote = {F1Fo ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a peripheral stalk. Proton flow through the Fo motor generates rotation of the central stalk, inducing conformational changes in the F1 motor that catalyzes ATP production. Here we present nine cryo-EM structures of E. coli ATP synthase to 3.1–3.4 Å resolution, in four discrete rotational sub-states, which provide a comprehensive structural model for this widely studied bacterial molecular machine. We observe torsional flexing of the entire complex and a rotational sub-step of Fo associated with long-range conformational changes that indicates how this flexibility accommodates the mismatch between the 3- and 10-fold symmetries of the F1 and Fo motors. We also identify density likely corresponding to lipid molecules that may contribute to the rotor/stator interaction within the Fo motor.},
doi = {10.1038/s41467-020-16387-2},
journal = {Nature Communications},
number = 1,
volume = 11,
place = {United States},
year = {Tue May 26 00:00:00 EDT 2020},
month = {Tue May 26 00:00:00 EDT 2020}
}
Works referenced in this record:
Analysis of an N-terminal deletion in subunit a of the Escherichia coli ATP synthase
journal, January 2017
- Ishmukhametov, Robert R.; DeLeon-Rangel, Jessica; Zhu, Shaotong
- Journal of Bioenergetics and Biomembranes, Vol. 49, Issue 2
Molecular Architecture of the Rotary Motor in ATP Synthase
journal, November 1999
- Stock, D.
- Science, Vol. 286, Issue 5445
On the appearance of carboxylates in electrostatic potential maps: ESP Involving Carboxylate Groups
journal, December 2016
- Wang, Jimin
- Protein Science, Vol. 26, Issue 3
ISOLDE : a physically realistic environment for model building into low-resolution electron-density maps
journal, April 2018
- Croll, Tristan Ian
- Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 6
Kinetic modeling of rotary CF0F1-ATP synthase: storage of elastic energy during energy transduction
journal, June 1999
- Pänke, Oliver; Rumberg, Bernd
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1412, Issue 2
Structure of a bacterial ATP synthase
journal, February 2019
- Guo, Hui; Suzuki, Toshiharu; Rubinstein, John L.
- eLife, Vol. 8
The proton pore in the Escherichia coli F0F1-ATPase: A requirement for arginine at position 210 of the a-subunit
journal, December 1987
- Lightowlers, R. N.; Howitt, S. M.; Hatch, L.
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 894, Issue 3
Impaired proton conductivity resulting from mutations in the a subunit of F1F0 ATPase in Escherichia coli.
journal, August 1986
- Cain, B. D.; Simoni, R. D.
- Journal of Biological Chemistry, Vol. 261, Issue 22
Inhibitory properties of endogenous subunit ϵ in the Escherichia coli F1 ATPase
journal, October 1979
- Laget, Patrice P.; Smith, Jeffrey B.
- Archives of Biochemistry and Biophysics, Vol. 197, Issue 1
Structure and Mechanisms of F-Type ATP Synthases
journal, June 2019
- Kühlbrandt, Werner
- Annual Review of Biochemistry, Vol. 88, Issue 1
Ultrafast purification and reconstitution of His-tagged cysteine-less Escherichia coli F1Fo ATP synthase
journal, January 2005
- Ishmukhametov, Robert R.; Galkin, Mikhail A.; Vik, Steven B.
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1706, Issue 1-2
Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F 1 -F o coupling
journal, June 2019
- Murphy, Bonnie J.; Klusch, Niklas; Langer, Julian
- Science, Vol. 364, Issue 6446
Solution structure of the N-terminal domain of the δ subunit of the E. coli ATPsynthase
journal, March 1997
- Wilkens, Stephan; Dunn, Stanley D.; Chandler, Jennifer
- Nature Structural Biology, Vol. 4, Issue 3
Horizontal membrane-intrinsic α-helices in the stator a-subunit of an F-type ATP synthase
journal, February 2015
- Allegretti, Matteo; Klusch, Niklas; Mills, Deryck J.
- Nature, Vol. 521, Issue 7551
HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures
journal, January 2008
- Ho, Bosco K.; Gruswitz, Franz
- BMC Structural Biology, Vol. 8, Issue 1
The dynamic stator stalk of rotary ATPases
journal, January 2012
- Stewart, Alastair G.; Lee, Lawrence K.; Donohoe, Mhairi
- Nature Communications, Vol. 3, Issue 1
The proton conducting F0-part of bacterial ATP synthases
journal, April 1984
- Hoppe, Jürgen; Sebald, Walter
- Biochimica et Biophysica Acta (BBA) - Reviews on Bioenergetics, Vol. 768, Issue 1
His15 of Subunit a of the Escherichia coli ATP Synthase Is Important for the Structure or Assembly of the Membrane Sector Fo
journal, August 1999
- Patterson, Annette Rochelle; Wada, Takaaki; Vik, Steven B.
- Archives of Biochemistry and Biophysics, Vol. 368, Issue 1
In vivo evidence for the role of the epsilon subunit as an inhibitor of the proton-translocating ATPase of Escherichia coli
journal, December 1984
- Klionsky, D. J.; Brusilow, W. S.; Simoni, R. D.
- Journal of Bacteriology, Vol. 160, Issue 3
Structure at 2.8 Â resolution of F1-ATPase from bovine heart mitochondria
journal, August 1994
- Abrahams, Jan Pieter; Leslie, Andrew G. W.; Lutter, René
- Nature, Vol. 370, Issue 6491
Transient accumulation of elastic energy in proton translocating ATP synthase
journal, April 1999
- Cherepanov, Dmitry A.; Mulkidjanian, Armen Y.; Junge, Wolfgang
- FEBS Letters, Vol. 449, Issue 1
Nucleotide-dependent and dicyclohexylcarbodiimide-sensitive conformational changes in the .epsilon. subunit of Escherichia coli ATP synthase
journal, November 1991
- Mendel-Hartvig, Janet; Capaldi, Roderick A.
- Biochemistry, Vol. 30, Issue 45
Structure of the ATP synthase catalytic complex (F1) from Escherichia coli in an autoinhibited conformation
journal, May 2011
- Cingolani, Gino; Duncan, Thomas M.
- Nature Structural & Molecular Biology, Vol. 18, Issue 6
ATP synthesis without R210 of subunit a in the Escherichia coli ATP synthase
journal, January 2008
- Ishmukhametov, Robert R.; Pond, J. Blake; Al-Huqail, Asma
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1777, Issue 1
Structural comparison of the vacuolar and Golgi V-ATPases from Saccharomyces cerevisiae
journal, March 2019
- Vasanthakumar, Thamiya; Bueler, Stephanie A.; Wu, Di
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 15
The Fo complex of the proton-translocating F-type ATPase of Escherichia coli.
journal, November 1992
- Deckers-Hebestreit, G.; Altendorf, K.
- Journal of Experimental Biology, Vol. 172, Issue 1
F1-ATPase of Escherichia coli
journal, March 2013
- Shah, Naman B.; Hutcheon, Marcus L.; Haarer, Brian K.
- Journal of Biological Chemistry, Vol. 288, Issue 13
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy
journal, February 2017
- Zheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul
- Nature Methods, Vol. 14, Issue 4
Rotary ATPases—dynamic molecular machines
journal, April 2014
- Stewart, Alastair G.; Laming, Elise M.; Sobti, Meghna
- Current Opinion in Structural Biology, Vol. 25
The role of interfacial lipids in stabilizing membrane protein oligomers
journal, January 2017
- Gupta, Kallol; Donlan, Joseph A. C.; Hopper, Jonathan T. S.
- Nature, Vol. 541, Issue 7637
How azide inhibits ATP hydrolysis by the F-ATPases
journal, May 2006
- Bowler, M. W.; Montgomery, M. G.; Leslie, A. G. W.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 23
Real-space refinement in PHENIX for cryo-EM and crystallography
journal, May 2018
- Afonine, Pavel V.; Poon, Billy K.; Read, Randy J.
- Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 6
Cryo-EM structures of the autoinhibited E. coli ATP synthase in three rotational states
journal, December 2016
- Sobti, Meghna; Smits, Callum; Wong, Andrew SW
- eLife, Vol. 5
Proton Translocation by the F1FOATPase of Escherichia coli
journal, February 1989
- Cain, B. D.; Simoni, R. D.
- Journal of Biological Chemistry, Vol. 264, Issue 6
Cryo-EM reveals distinct conformations of E. coli ATP synthase on exposure to ATP
journal, March 2019
- Sobti, Meghna; Ishmukhametov, Robert; Bouwer, James C.
- eLife, Vol. 8
High-resolution cryo-EM analysis of the yeast ATP synthase in a lipid membrane
journal, April 2018
- Srivastava, Anurag P.; Luo, Min; Zhou, Wenchang
- Science, Vol. 360, Issue 6389
Interaction between Glu-219 and His-245 within the a subunit of F1F0-ATPase in Escherichia coli.
journal, May 1988
- Cain, B. D.; Simoni, R. D.
- Journal of Biological Chemistry, Vol. 263, Issue 14
The ATP synthase: the understood, the uncertain and the unknown
journal, January 2013
- Walker, John E.
- Biochemical Society Transactions, Vol. 41, Issue 1
ATP Synthase b Subunit Dimerization Domain: A Right-Handed Coiled Coil with Offset Helices
journal, December 2006
- Del Rizzo, Paul A.; Bi, Yumin; Dunn, Stanley D.
- Journal of Molecular Biology, Vol. 364, Issue 4
Cross-linking and electron microscopy studies of the structure and functioning of the Escherichia coli ATP synthase
journal, January 2000
- Capaldi, R. A.; Schulenberg, B.; Murray, J.
- Journal of Experimental Biology, Vol. 203, Issue 1
Cryo-EM structure of the mammalian ATP synthase tetramer bound with inhibitory protein IF1
journal, June 2019
- Gu, Jinke; Zhang, Laixing; Zong, Shuai
- Science, Vol. 364, Issue 6445
Structure of a mitochondrial ATP synthase with bound native cardiolipin
journal, November 2019
- Mühleip, Alexander; McComas, Sarah E.; Amunts, Alexey
- eLife, Vol. 8
Cryo-EM analysis of a domain antibody bound rotary ATPase complex
journal, March 2017
- Davies, Roberta B.; Smits, Callum; Wong, Andrew S. W.
- Journal of Structural Biology, Vol. 197, Issue 3
Structural Asymmetry and Kinetic Limping of Single Rotary F-ATP Synthases
journal, January 2019
- Sielaff, Hendrik; Yanagisawa, Seiga; Frasch, Wayne D.
- Molecules, Vol. 24, Issue 3
A mechanism of proton translocation by F1F0 ATP synthases suggested by double mutants of the a subunit.
journal, December 1994
- Vik, S. B.; Antonio, B. J.
- Journal of Biological Chemistry, Vol. 269, Issue 48
RELION: Implementation of a Bayesian approach to cryo-EM structure determination
journal, December 2012
- Scheres, Sjors H. W.
- Journal of Structural Biology, Vol. 180, Issue 3, p. 519-530
Features and development of Coot
journal, March 2010
- Emsley, P.; Lohkamp, B.; Scott, W. G.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
The regulatory subunit ε in Escherichia coli FOF1-ATP synthase
journal, September 2018
- Sielaff, Hendrik; Duncan, Thomas M.; Börsch, Michael
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1859, Issue 9
The atp Synthase—A Splendid Molecular Machine
journal, June 1997
- Boyer, Paul D.
- Annual Review of Biochemistry, Vol. 66, Issue 1
Atomic model for the dimeric F O region of mitochondrial ATP synthase
journal, October 2017
- Guo, Hui; Bueler, Stephanie A.; Rubinstein, John L.
- Science, Vol. 358, Issue 6365
Spotlighting motors and controls of single FoF1-ATP synthase
journal, September 2013
- Börsch, Michael; Duncan, Thomas M.
- Biochemical Society Transactions, Vol. 41, Issue 5
Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM
journal, October 2015
- Zhou, Anna; Rohou, Alexis; Schep, Daniel G.
- eLife, Vol. 4
Structure, mechanism, and regulation of the chloroplast ATP synthase
journal, May 2018
- Hahn, Alexander; Vonck, Janet; Mills, Deryck J.
- Science, Vol. 360, Issue 6389
The proton pore in the Escherichia coli F0F1-ATPase: Substitution of glutamate by glutamine at position 219 of the a-subunit prevents F0-mediated proton permeability
journal, April 1988
- Lightowlers, Robert N.; Howitt, Susan M.; Hatch, Lyndall
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 933, Issue 2
Cardiolipin binds selectively but transiently to conserved lysine residues in the rotor of metazoan ATP synthases
journal, July 2016
- Duncan, Anna L.; Robinson, Alan J.; Walker, John E.
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 31
Identifying key membrane protein lipid interactions using mass spectrometry
journal, April 2018
- Gupta, Kallol; Li, Jingwen; Liko, Idlir
- Nature Protocols, Vol. 13, Issue 5
Complete Ion-Coordination Structure in the Rotor Ring of Na+-Dependent F-ATP Synthases
journal, August 2009
- Meier, Thomas; Krah, Alexander; Bond, Peter J.
- Journal of Molecular Biology, Vol. 391, Issue 2
The Essential Arginine Residue at Position 210 in the a Subunit of the Escherichia coli ATP Synthase Can Be Transferred to Position 252 with Partial Retention of Activity
journal, December 1995
- Hatch, Lyndall P.; Cox, Graeme B.; Howitt, Susan M.
- Journal of Biological Chemistry, Vol. 270, Issue 49
Insights into the Molecular Mechanism of Rotation in the Fo Sector of ATP Synthase
journal, March 2004
- Aksimentiev, Aleksij; Balabin, Ilya A.; Fillingame, Robert H.
- Biophysical Journal, Vol. 86, Issue 3