the sub-nanometer resolution and perhaps atomic-resolution structures of proteins
and protein complexes in vivo. This methodology called the cellular tomography,
although not the scope of this chapter, is a promising future technology for
atomic-resolution structures of proteins and protein complexes in its native environment “the cell.” With the advent of phase plates, energy filters, and automation
in cryo-EM data collection, promising efforts are being made to achieve that goal
and the realization of that goal may not be far away which would in turn potentially
further accelerate the SBDD program.
Acknowledgements RN was supported by Ramalingaswamy Fellowship from DBT. RN would
like to thank his laboratory members and colleagues for their constant support, valuable scientific
and technical discussion. Last but not least, RN would like to thank IISER-TVM past Director
Prof. ED Jemmis and present Director Prof. V. Ramakrishnan for their unstinted support.
References
1. Dauter Z, Lamzin VS, Wilson KS (1995) Proteins at atomic resolution. Curr Opin Struct
Biol 5:784–790
2. Kozma D, Simon I, Tusnady GE (2013) PDBTM: protein data bank of transmembrane
proteins after 8 years. Nucleic Acids Res 41:D524–D529
3. Natesh R (2014) Crystallography beyond crystals: PX and SP cryoEM. Resonance 19:
1177–1196
4. Mountain V (2003) Astex, structural genomix, and syrrx. i can see clearly now: structural
biology and drug discovery. Chem Biol 10:95–98
5. Bartesaghi A, Merk A, Banerjee S, Matthies D, Wu X, Milne JL, Subramaniam S (2015) A
resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant
inhibitor. Science 348:1147–1151
6. Merk A, Bartesaghi A, Banerjee S, Falconieri V, Rao P, Davis MI, Pragani R, Boxer MB,
Earl LA, Milne JLS, Subramaniam S (2016) Breaking cryo-EM resolution barriers to
facilitate drug discovery. Cell 165:1698–1707
7. Shalev-Benami M, Zhang Y, Rozenberg H, Nobe Y, Taoka M, Matzov D, Zimmerman E,
Bashan A, Isobe T, Jaffe CL, Yonath A, Skiniotis G (2017) Atomic resolution snapshot of
Leishmania ribosome inhibition by the aminoglycoside paromomycin. Nat Commun 8:1589
8. Dong Y, Liu Y, Jiang W, Smith TJ, Xu Z, Rossmann MG (2017) Antibody-induced
uncoating of human rhinovirus B14. In: Proceedings of the national academy of sciences of
the United States of America, vol 114, pp 8017–8022
9. Danev R, Tegunov D, Baumeister W (2017) Using the Volta phase plate with defocus for
cryo-EM single particle analysis. Elife 6:1–9
10. Banerjee S, Bartesaghi A, Merk A, Rao P, Bulfer SL, Yan Y, Green N, Mroczkowski B,
Neitz RJ, Wipf P, Falconieri V, Deshaies RJ, Milne JL, Huryn D, Arkin M, Subramaniam S
(2016) A resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition.
Science 351:871–875
11. Dubochet J, Mcdowall AW (1981) Vitrification of pure water for electron-microscopy.
J Microsc Oxford 124:Rp3–Rp4
12. Vogel RH, Provencher SW, von Bonsdorff CH, Adrian M, Dubochet J (1986) Envelope
structure of Semliki Forest virus reconstructed from cryo-electron micrographs. Nature
320:533–535
13. Henderson R, Unwin PN (1975) Three-dimensional model of purple membrane obtained by
electron microscopy. Nature 257:28–32
Single-Particle cryo-EM as a Pipeline for Obtaining Atomic …
395
and protein complexes in vivo. This methodology called the cellular tomography,
although not the scope of this chapter, is a promising future technology for
atomic-resolution structures of proteins and protein complexes in its native environment “the cell.” With the advent of phase plates, energy filters, and automation
in cryo-EM data collection, promising efforts are being made to achieve that goal
and the realization of that goal may not be far away which would in turn potentially
further accelerate the SBDD program.
Acknowledgements RN was supported by Ramalingaswamy Fellowship from DBT. RN would
like to thank his laboratory members and colleagues for their constant support, valuable scientific
and technical discussion. Last but not least, RN would like to thank IISER-TVM past Director
Prof. ED Jemmis and present Director Prof. V. Ramakrishnan for their unstinted support.
References
1. Dauter Z, Lamzin VS, Wilson KS (1995) Proteins at atomic resolution. Curr Opin Struct
Biol 5:784–790
2. Kozma D, Simon I, Tusnady GE (2013) PDBTM: protein data bank of transmembrane
proteins after 8 years. Nucleic Acids Res 41:D524–D529
3. Natesh R (2014) Crystallography beyond crystals: PX and SP cryoEM. Resonance 19:
1177–1196
4. Mountain V (2003) Astex, structural genomix, and syrrx. i can see clearly now: structural
biology and drug discovery. Chem Biol 10:95–98
5. Bartesaghi A, Merk A, Banerjee S, Matthies D, Wu X, Milne JL, Subramaniam S (2015) A
resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant
inhibitor. Science 348:1147–1151
6. Merk A, Bartesaghi A, Banerjee S, Falconieri V, Rao P, Davis MI, Pragani R, Boxer MB,
Earl LA, Milne JLS, Subramaniam S (2016) Breaking cryo-EM resolution barriers to
facilitate drug discovery. Cell 165:1698–1707
7. Shalev-Benami M, Zhang Y, Rozenberg H, Nobe Y, Taoka M, Matzov D, Zimmerman E,
Bashan A, Isobe T, Jaffe CL, Yonath A, Skiniotis G (2017) Atomic resolution snapshot of
Leishmania ribosome inhibition by the aminoglycoside paromomycin. Nat Commun 8:1589
8. Dong Y, Liu Y, Jiang W, Smith TJ, Xu Z, Rossmann MG (2017) Antibody-induced
uncoating of human rhinovirus B14. In: Proceedings of the national academy of sciences of
the United States of America, vol 114, pp 8017–8022
9. Danev R, Tegunov D, Baumeister W (2017) Using the Volta phase plate with defocus for
cryo-EM single particle analysis. Elife 6:1–9
10. Banerjee S, Bartesaghi A, Merk A, Rao P, Bulfer SL, Yan Y, Green N, Mroczkowski B,
Neitz RJ, Wipf P, Falconieri V, Deshaies RJ, Milne JL, Huryn D, Arkin M, Subramaniam S
(2016) A resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition.
Science 351:871–875
11. Dubochet J, Mcdowall AW (1981) Vitrification of pure water for electron-microscopy.
J Microsc Oxford 124:Rp3–Rp4
12. Vogel RH, Provencher SW, von Bonsdorff CH, Adrian M, Dubochet J (1986) Envelope
structure of Semliki Forest virus reconstructed from cryo-electron micrographs. Nature
320:533–535
13. Henderson R, Unwin PN (1975) Three-dimensional model of purple membrane obtained by
electron microscopy. Nature 257:28–32
Single-Particle cryo-EM as a Pipeline for Obtaining Atomic …
395