Abstract
In single-particle cryo-electron microscopy (cryo-EM), molecules suspended in a thin aqueous layer are rapidly frozen and imaged at cryogenic temperature in the transmission electron microscope. From the random projection views, a three-dimensional image is reconstructed, enabling the structure of the molecule to be obtained. In this article I discuss technological progress over the past decade, which has, in my own field of study, culminated in the determination of ribosome structure at 2.5-Å resolution. I also discuss likely future improvements in methodology.
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References
Grassucci, R.A., Taylor, D.J. & Frank, J. Preparation of macromolecular complexes for cryo-electron microscopy. Nat. Protoc. 2, 3239–3246 (2007).
Grassucci, R.A., Taylor, D. & Frank, J. Visualization of macromolecular complexes using cryo-electron microscopy with FEI Tecnai transmission electron microscopes. Nat. Protoc. 3, 330–339 (2008).
Shaikh, T.R. et al. SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat. Protoc. 3, 1941–1974 (2008).
Trabuco, L.G., Villa, E., Mitra, K., Frank, J. & Schulten, K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16, 673–683 (2008).
Scheres, S.H.W. et al. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nat. Methods 4, 27–29 (2007).
Scheres, S.H.W. A Bayesian view on cryo-EM structure determination. J. Mol. Biol. 415, 406–418 (2012).
Zhang, X., Jin, L., Fang, Q., Hui, W.H. & Zhou, Z.H. 3.3 A cryo-EM structure of a nonenveloped virus reveals a priming mechanism for cell entry. Cell 141, 472–482 (2010).
LeBarron, J. et al. Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome. J. Struct. Biol. 164, 24–32 (2008).
Villa, E. et al. Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proc. Natl. Acad. Sci. USA 106, 1063–1068 (2009).
Hashem, Y. et al. High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature 494, 385–389 (2013).
Henderson, R. The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules. Q. Rev. Biophys. 28, 171–193 (1995).
Frank, J. et al. A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome. Nature 376, 441–444 (1995).
Bai, X.C., Fernandez, I.S., McMullan, G. & Scheres, S.H.W. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles. eLife 2, e00461 (2013).
Liu, Z. et al. Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit. Proc. Natl. Acad. Sci. USA 113, 12174–12179 (2016).
Liao, M., Cao, E., Julius, D. & Cheng, Y. Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504, 107–112 (2013).
Cao, E., Liao, M., Cheng, Y. & Julius, D. TRPV1 structures in distinct conformations reveal activation mechanisms. Nature 504, 113–118 (2013).
Jain, T., Sheehan, P., Crum, J., Carragher, B. & Potter, C.S. Spotiton: a prototype for an integrated inkjet dispense and vitrification system for cryo-TEM. J. Struct. Biol. 179, 68–75 (2012).
Razinkov, I. et al. A new method for vitrifying samples for cryoEM. J. Struct. Biol. 195, 190–198 (2016).
Russo, C.J. & Passmore, L.A. Electron microscopy: ultrastable gold substrates for electron cryomicroscopy. Science 346, 1377–1380 (2014).
Russo, C.J. & Passmore, L.A. Progress towards an optimal specimen support for electron cryomicroscopy. Curr. Opin. Struct. Biol. 37, 81–89 (2016).
Crowther, R.A. (ed.) The Resolution Revolution: Recent Advances in CryoEM (Methods in Enzymology Volume 579)(Academic Press/Elsevier, 2016).
Danev, R. & Baumeister, W. Cryo-EM single particle analysis with the Volta phase plate. eLife 5, e13046 (2016).
Lu, Z. et al. Monolithic microfluidic mixing-spraying devices for time-resolved cryo-electron microscopy. J. Struct. Biol. 168, 388–395 (2009).
Chen, B. et al. Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryogenic electron microscopy. Structure 23, 1097–1105 (2015).
Fu, Z. et al. Key intermediates in ribosome recycling visualized by time-resolved cryoelectron microscopy. Structure 24, 2092–2101 (2016).
Bai, X., Rajendra, E., Yang, G., Shi, Y. & Scheres, S.H.W. Sampling the conformational space of the catalytic subunit of human g-secretase. eLife 4, e11182 (2015).
Liu, Z. et al. Determination of the ribosome structure to a resolution of 2.5 Å by single-particle cryo-EM. Protein Sci. http://dx.doi.org/10.1002/pro.306 (2016).
Schüler, M. et al. Structure of the ribosome-bound cricket paralysis virus IRES RNA. Nat. Struct. Mol. Biol. 13, 1092–1096 (2006).
Armache, J.P. et al. Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution. Proc. Natl. Acad. Sci. USA 107, 19748–19753 (2010).
Wong, W. et al. Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine. eLife 3, e03080 (2014).
Acknowledgements
This work has been supported by the Howard Hughes Medical Institute and by US National Institutes of Health grant R01 GM29169.
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Frank, J. Advances in the field of single-particle cryo-electron microscopy over the last decade. Nat Protoc 12, 209–212 (2017). https://doi.org/10.1038/nprot.2017.004
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DOI: https://doi.org/10.1038/nprot.2017.004
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