Acknowledgments
Calculations were performed at sciCORE (http://scicore.unibas.
ch/) scientific computing center at University of Basel. RDR
acknowledges funding from the Fellowships for Excellence program sponsored by the Werner-Siemens Foundation and the University of Basel. This work was supported by the Swiss National
Science Foundation through grant 205320_166164 and the
NCCR TransCure.
References
1. Henderson R, Unwin PNT (1975) Threedimensional model of purple membrane
obtained by electron microscopy. Nature
257:28–32
2. Adrian M, Dubochet J, Lepault J, McDowall
AW (1984) Cryo-electron microscopy of
viruses. Nature 308:32–36
3. Henderson R, Baldwin JMM, Ceska TAA et al
(1990) Model for the structure of bacteriorhodopsin based on high-resolution electron cryomicroscopy. J Mol Biol 213:899–929
4. Ku ¨hlbrandt W, Wang DN, Fujiyoshi Y (1994)
Atomic model of plant light-harvesting complex by electron crystallography. Nature
367:614–621
5. Nogales E, Wolf SG, Downing KH (1998)
Structure of the αβ tubulin dimer by electron
crystallography. Nature 391:199–203
6. Gonen T, Cheng Y, Sliz P et al (2005) Lipidprotein interactions in double-layered two-dimensional
AQP0
crystals.
Nature
438:633–638
7. Deisenhofer J, Michel H (1989) The photosynthetic reaction center from the purple bacterium Rhodopseudomonas viridis. Science
245:1463–1473
8. Landau EM, Rosenbusch JP (1996) Lipidic
cubic phases: a novel concept for the crystallization of membrane proteins. Proc Natl Acad
Sci U S A 93:14532–14535
9. Liang B, Tamm LK (2016) NMR as a tool to
investigate the structure, dynamics and function of membrane proteins. Nat Struct Mol
Biol 23:468
10. Frank J (2006) Three-dimensional Electron
microscopy of macromolecular assemblies,
2nd edn. Oxford University Press, Oxford
11. Ku ¨hlbrandt W (2014) The resolution revolution. Science 343:1443–1444
12. Liao M, Cao E, Julius D, Cheng Y (2013)
Structure of the TRPV1 ion channel
determined by electron cryo-microscopy.
Nature 504:107–112
13. Gao Y, Cao E, Julius D, Cheng Y (2016)
TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action. Nature
534:347–351
14. Goni GM, Epifano C, Boskovic J et al (2014)
Phosphatidylinositol 4,5-bisphosphate triggers
activation of focal adhesion kinase by inducing
clustering and conformational changes. Proc
Natl Acad Sci 111:E3177–E3186
15. Gonen S, DiMaio F, Gonen T, Baker D (2015)
Design of ordered two-dimensional arrays
mediated by noncovalent protein-protein
interfaces. Science 348:1365–1368
16. Subramanian RH, Smith SJ, Alberstein RG
et al (2018) Self-assembly of a designed nucleoprotein architecture through multimodal
interactions. ACS Cent Sci 4:1578–1586
17. Schenk AD, Castan ˜o-Dı ´ez D, Gipson B et al
(2010) 3D reconstruction from 2D crystal
image and diffraction data. In: Enzymology
GJJBT-M in Cryo-EM, part B: 3-D reconstruction. Academic Press, New York, pp
101–129
18. De Rosier DJ, Klug A (1968) Reconstruction
of three dimensional structures from Electron
micrographs. Nature 217:130–134
19. Stahlberg H, Biyani N, Engel A (2015) 3D
reconstruction of two-dimensional crystals.
Arch Biochem Biophys 581:68–77
20. Crowther RA, Henderson R, Smith JM (1996)
MRC image processing programs. J Struct Biol
116:9–16
21. Gipson B, Zeng X, Zhang ZY, Stahlberg H
(2007) 2dx—user-friendly image processing
for 2D crystals. J Struct Biol 157:64–72
22. Biyani N, Righetto RD, McLeod R et al (2017)
Focus: the interface between data collection
and data processing in cryo-EM. J Struct Biol
198:124–133
282
Ricardo Righetto and Henning Stahlberg
Calculations were performed at sciCORE (http://scicore.unibas.
ch/) scientific computing center at University of Basel. RDR
acknowledges funding from the Fellowships for Excellence program sponsored by the Werner-Siemens Foundation and the University of Basel. This work was supported by the Swiss National
Science Foundation through grant 205320_166164 and the
NCCR TransCure.
References
1. Henderson R, Unwin PNT (1975) Threedimensional model of purple membrane
obtained by electron microscopy. Nature
257:28–32
2. Adrian M, Dubochet J, Lepault J, McDowall
AW (1984) Cryo-electron microscopy of
viruses. Nature 308:32–36
3. Henderson R, Baldwin JMM, Ceska TAA et al
(1990) Model for the structure of bacteriorhodopsin based on high-resolution electron cryomicroscopy. J Mol Biol 213:899–929
4. Ku ¨hlbrandt W, Wang DN, Fujiyoshi Y (1994)
Atomic model of plant light-harvesting complex by electron crystallography. Nature
367:614–621
5. Nogales E, Wolf SG, Downing KH (1998)
Structure of the αβ tubulin dimer by electron
crystallography. Nature 391:199–203
6. Gonen T, Cheng Y, Sliz P et al (2005) Lipidprotein interactions in double-layered two-dimensional
AQP0
crystals.
Nature
438:633–638
7. Deisenhofer J, Michel H (1989) The photosynthetic reaction center from the purple bacterium Rhodopseudomonas viridis. Science
245:1463–1473
8. Landau EM, Rosenbusch JP (1996) Lipidic
cubic phases: a novel concept for the crystallization of membrane proteins. Proc Natl Acad
Sci U S A 93:14532–14535
9. Liang B, Tamm LK (2016) NMR as a tool to
investigate the structure, dynamics and function of membrane proteins. Nat Struct Mol
Biol 23:468
10. Frank J (2006) Three-dimensional Electron
microscopy of macromolecular assemblies,
2nd edn. Oxford University Press, Oxford
11. Ku ¨hlbrandt W (2014) The resolution revolution. Science 343:1443–1444
12. Liao M, Cao E, Julius D, Cheng Y (2013)
Structure of the TRPV1 ion channel
determined by electron cryo-microscopy.
Nature 504:107–112
13. Gao Y, Cao E, Julius D, Cheng Y (2016)
TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action. Nature
534:347–351
14. Goni GM, Epifano C, Boskovic J et al (2014)
Phosphatidylinositol 4,5-bisphosphate triggers
activation of focal adhesion kinase by inducing
clustering and conformational changes. Proc
Natl Acad Sci 111:E3177–E3186
15. Gonen S, DiMaio F, Gonen T, Baker D (2015)
Design of ordered two-dimensional arrays
mediated by noncovalent protein-protein
interfaces. Science 348:1365–1368
16. Subramanian RH, Smith SJ, Alberstein RG
et al (2018) Self-assembly of a designed nucleoprotein architecture through multimodal
interactions. ACS Cent Sci 4:1578–1586
17. Schenk AD, Castan ˜o-Dı ´ez D, Gipson B et al
(2010) 3D reconstruction from 2D crystal
image and diffraction data. In: Enzymology
GJJBT-M in Cryo-EM, part B: 3-D reconstruction. Academic Press, New York, pp
101–129
18. De Rosier DJ, Klug A (1968) Reconstruction
of three dimensional structures from Electron
micrographs. Nature 217:130–134
19. Stahlberg H, Biyani N, Engel A (2015) 3D
reconstruction of two-dimensional crystals.
Arch Biochem Biophys 581:68–77
20. Crowther RA, Henderson R, Smith JM (1996)
MRC image processing programs. J Struct Biol
116:9–16
21. Gipson B, Zeng X, Zhang ZY, Stahlberg H
(2007) 2dx—user-friendly image processing
for 2D crystals. J Struct Biol 157:64–72
22. Biyani N, Righetto RD, McLeod R et al (2017)
Focus: the interface between data collection
and data processing in cryo-EM. J Struct Biol
198:124–133
282
Ricardo Righetto and Henning Stahlberg