Conventional electron microscopy, cryo-electron microscopy and cryo-electron tomography of viruses

Subcellular Biochemistry

Volumn 68, Issue , 2013, Pages 79-115

  Castón, José R ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

Capsid; Cryo electron microscopy; Cryo electron tomography; Electron microscopy; Fourier transform; Image processing; Resolution; Three dimensional reconstruction; Viral macromolecular assembly; Virus

Indexed keywords

ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; CRYOELECTRON MICROSCOPY; ELECTRON TOMOGRAPHY; HUMAN; REVIEW; ULTRASTRUCTURE; VIRUS;

ANIMALS; CRYOELECTRON MICROSCOPY; ELECTRON MICROSCOPE TOMOGRAPHY; HUMANS; MODELS, MOLECULAR; VIRUSES;

EID: 84904846139     PISSN: 03060225     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-94-007-6552-8_3     Document Type: Article

References (62)

1. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2007) Molecular biology of the cell. Garland Science, New York
2. Nogales E, Grigorieff N (2001) Molecular machines: putting the pieces together. J Cell Biol 152:F1-F10
3. Steven A, Belnap D (2005) Electron microscopy and image processing: an essential tool for structural analysis of macromolecules. Curr Protoc Protein Sci Chapter 17:Unit 17 12
4. Klug A (2010) From virus structure to chromatin: X-ray diffraction to three-dimensional electron microscopy. Annu Rev Biochem 79:1-35
5. Harrison SC (2004) Whither structural biology? Nat Struct Mol Biol 11:12-15
6. Baumeister W, Steven AC (2000) Macromolecular electron microscopy in the era of structural genomics. Trends Biochem Sci 25:624-631
7. Steven AC, Baumeister W (2008) The future is hybrid. J Struct Biol 163:186-195
8. Lasker K, Phillips JL, Russel D, Velazquez-Muriel J, Schneidman-Duhovny D, Tjioe E, Webb B, Schlessinger A, Sali A (2010) Integrative structure modeling of macromolecular assemblies from proteomics data. Mol Cell Proteomics 9:1689-1702
9. Goldsmith CS, Miller SE (2009) Modern uses of electron microscopy for detection of viruses. Clin Microbiol Rev 22:552-563
10. Bozzola JJ, Russell LD (1999) Electron microscopy. Principles and techniques for biologist. Jones and Bartlett Publishers, Boston
11. Dubochet J, Adrian M, Chang JJ, Homo JC, Lepault J, McDowall AW, Schultz P (1988) Cryoelectron microscopy of vitrified specimens. Q Rev Biophys 21:129-228
12. Amos LA, Henderson R, Unwin PN (1982) Three-dimensional structure determination by electron microscopy of two-dimensional crystals. Prog Biophys Mol Biol 39:183-231
13. Henderson R (2004) Realizing the potential of electron cryo-microscopy. Q Rev Biophys 37:3-13
14. Harris JR (1997) Negative staining and cryoelectron microscopy: the thin film techniques. BIOS Scientific Publishers Ltd., Oxford
15. Wild P (2008) Electron microscopy of viruses and virus-cell interactions. Methods Cell Biol 88:497-524
16. Leiman PG, Kanamaru S, Mesyanzhinov VV, Arisaka F, Rossmann MG (2003) Structure and morphogenesis of bacteriophage T4. Cell Mol Life Sci 60:2356-2370
17. Cavalier A, Spehner D, Humbel BM (eds) (2008) Handbook of cryo-preparation methods for electron microscopy. CRC Press, London
18. Baker TS, Olson NH, Fuller SD (1999) Adding the third dimension to virus life cycles: threedimensional reconstruction of icosahedral viruses from cryo-electron micrographs. Microbiol Mol Biol Rev 63:862-922
19. De Carlo S, Stark H (2010) Cryonegative staining of macromolecular assemblies. Methods Enzymol 481:127-145
20. Crowther RA (2008) The Leeuwenhoek lecture 2006. Microscopy goes cold: frozen viruses reveal their structural secrets. Philos Trans R Soc Lond B Biol Sci 363:2441-2451
21. De Rosier DJ, Klug A (1968) Reconstruction of three dimensional structures from electron micrographs. Nature 217:130-134
22. Moody MF (1990) Image analysis of electron micrographs. In: Hawkes PW, Valdré U (eds) Biophysical electron microscopy. Basis concepts and modern techniques. Academic Press, London, pp 145-288
23. Rochat RH, Chiu W (2012) Cryo-electron microscopy and tomography of virus particles. In: Egelman EH (ed) Comprehensive biophysics, biophysical techniques for structural characterization of macromolecules, vol 1. Academic Press, Oxford, pp 311-340
24. Chang J, Liu X, Rochat RH, Baker ML, Chiu W (2012) Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography. Adv Exp Med Biol 726:49-90
25. Grigorieff N, Harrison SC (2011) Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy. Curr Opin Struct Biol 21:265-273
26. Steven AC, Heymann JB, Cheng N, Trus BL, Conway JF (2005) Virus maturation: dynamics and mechanism of a stabilizing structural transition that leads to infectivity. Curr Opin Struct Biol 15:227-236
27. Luque D, Gonzalez JM, Garriga D, Ghabrial SA, Havens WM, Trus B, Verdaguer N, Carrascosa JL, Castón JR (2010) The T=1 capsid protein of penicillium chrysogenum virus is formed by a repeated helix-rich core indicative of gene duplication. J Virol 84:7256-7266
28. Johnson JE (2008) Multi-disciplinary studies of viruses: the role of structure in shaping the questions and answers. J Struct Biol 163:246-253
29. Russel D, Lasker K, Phillips J, Schneidman-Duhovny D, Velazquez-Muriel JA, Sali A (2009) The structural dynamics of macromolecular processes. Curr Opin Cell Biol 21:97-108
30. Tang L, Johnson JE (2002) Structural biology of viruses by the combination of electron cryomicroscopy and X-ray crystallography. Biochemistry 41:11517-11524
31. Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A (2008) Protein structure fitting and refinement guided by cryo-EM density. Structure 16:295-307
32. Rossmann MG, Morais MC, Leiman PG, Zhang W (2005) Combining X-ray crystallography and electron microscopy. Structure 13:355-362
33. Topf M, Sali A (2005) Combining electron microscopy and comparative protein structure modeling. Curr Opin Struct Biol 15:578-585
34. Luque D, Saugar I, Rodriguez JF, Verdaguer N, Garriga D, Martin CS, Velazquez-Muriel JA, Trus BL, Carrascosa JL, Castón JR (2007) Infectious bursal disease virus capsid assembly and maturation by structural rearrangements of a transient molecular switch. J Virol 81:6869-6878
35. Zhou ZH (2011) Atomic resolution cryo electron microscopy of macromolecular complexes. Adv Protein Chem Struct Biol 82:1-35
36. Zhou ZH (2008) Towards atomic resolution structural determination by single-particle cryoelectron microscopy. Curr Opin Struct Biol 18:218-228
37. Hryc CF, Chen DH, Chiu W (2011) Near-atomic-resolution cryo-EM for molecular virology. Curr Opin Virol 1:110-117
38. Yu X, Jin L, Zhou ZH (2008) 3.88 A structure of cytoplasmic polyhedrosis virus by cryoelectron microscopy. Nature 453:415-419
39. Zhang X, Settembre E, Xu C, Dormitzer PR, Bellamy R, Harrison SC, Grigorieff N (2008) Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proc Natl Acad Sci U S A 105:1867-1872
40. Briggs JA, Huiskonen JT, Fernando KV, Gilbert RJ, Scotti P, Butcher SJ, Fuller SD (2005) Classification and three-dimensional reconstruction of unevenly distributed or symmetry mismatched features of icosahedral particles. J Struct Biol 150:332-339
41. Kostyuchenko VA, Chipman PR, Leiman PG, Arisaka F, Mesyanzhinov VV, Rossmann MG (2005) The tail structure of bacteriophage T4 and its mechanism of contraction. Nat Struct Mol Biol 12:810-813
42. Aksyuk AA, Rossmann MG (2011) Bacteriophage assembly. Viruses 3:172-203
43. Stubbs G, Kendall A (2012) Helical viruses. Adv Exp Med Biol 726:631-658
44. Ge P, Tsao J, Schein S, Green TJ, Luo M, Zhou ZH (2010) Cryo-EM model of the bulletshaped vesicular stomatitis virus. Science 327:689-693
45. Ge P, Zhou ZH (2011) Hydrogen-bonding networks and RNA bases revealed by cryo electron microscopy suggest a triggering mechanism for calcium switches. Proc Natl Acad Sci U S A 108:9637-9642
46. Egelman EH (2007) Single-particle reconstruction from EM images of helical filaments. Curr Opin Struct Biol 17:556-561
47. Grunewald K, Medalia O, Gross A, Steven AC, Baumeister W (2003) Prospects of electron cryotomography to visualize macromolecular complexes inside cellular compartments: implications of crowding. Biophys Chem 100:577-591
48. Lucic V, Forster F, BaumeisterW(2005) Structural studies by electron tomography: from cells to molecules. Annu Rev Biochem 74:833-865
49. Cope J, Heumann J, Hoenger A (2011) Cryo-electron tomography for structural characterization of macromolecular complexes. Curr Protoc Protein Sci Chapter 17:Unit17 13
50. Subramaniam S, Bartesaghi A, Liu J, Bennett AE, Sougrat R (2007) Electron tomography of viruses. Curr Opin Struct Biol 17:596-602
51. Grunewald K, Cyrklaff M (2006) Structure of complex viruses and virus-infected cells by electron cryo tomography. Curr Opin Microbiol 9:437-442
52. Grunewald K, Desai P, Winkler DC, Heymann JB, Belnap DM, Baumeister W, Steven AC (2003) Three-dimensional structure of herpes simplex virus from cryo-electron tomography. Science 302:1396-1398
53. Butan C, Winkler DC, Heymann JB, Craven RC, Steven AC (2008) RSV capsid polymorphism correlates with polymerization efficiency and envelope glycoprotein content: implications that nucleation controls morphogenesis. J Mol Biol 376:1168-1181
54. Harris A, Cardone G, Winkler DC, Heymann JB, Brecher M, White JM, Steven AC (2006) Influenza virus pleiomorphy characterized by cryoelectron tomography. Proc Natl Acad Sci U S A 103:19123-19127
55. Cyrklaff M, Risco C, Fernandez JJ, Jimenez MV, Esteban M, Baumeister W, Carrascosa JL (2005) Cryo-electron tomography of vaccinia virus. Proc Natl Acad Sci U S A 102:2772-2777
56. Ibiricu I, Huiskonen JT, Dohner K, Bradke F, Sodeik B, Grunewald K (2011) Cryo electron tomography of herpes simplex virus during axonal transport and secondary envelopment in primary neurons. PLoS Pathog 7:e1002406
57. Fu CY, Johnson JE (2011) Viral life cycles captured in three-dimensions with electron microscopy tomography. Curr Opin Virol 1:125-133
58. Iwasaki K, Omura T (2010) Electron tomography of the supramolecular structure of virusinfected cells. Curr Opin Struct Biol 20:632-639
59. Crowther RA, Amos LA, Finch JT, De Rosier DJ, Klug A (1970) Three dimensional reconstructions of spherical viruses by fourier synthesis from electron micrographs. Nature 226:421-425
60. Agbandje-McKenna M, McKenna R (eds) (2011) Structural virology. RSC Publishing, Cambridge
61. Jensen GJ (ed) (2010) Cryo-EM, Part A. Sample preparation and data collection. Methods in Enzymology, vol 481; Cryo-EM, part B. 3-D Reconstruction. Methods in Enzymology, vol 482; Cryo-EM, part C. Analysis, interpretation and case studies. Methods in Enzymology, vol 483. Academic Press
62. Rossmann MG, Rao VB (eds) (2012) Viral molecular machines. Adv Exp Med Biol, vol 726. Springer, New York