Cryoelectron microscopy of icosahedral virus particles

Methods in Molecular Biology

Volumn 369, Issue , 2007, Pages 345-363

  Jiang, Wen ^a   Chiu, Wah ^a  

^a NONE

Author keywords

3D reconstruction; Cryo EM; Cryoelectron microscopy; Icosahedral virus; Secondary structure elements; Structural fitting; Subnanometer resolution

Indexed keywords

MIRIDAE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; CRYOELECTRON MICROSCOPY; FREEZING; METHODOLOGY; PLANT VIRUS; REOVIRUS; THREE DIMENSIONAL IMAGING; ULTRASTRUCTURE; VIRION;

CRYOELECTRON MICROSCOPY; FREEZING; IMAGING, THREE-DIMENSIONAL; MODELS, MOLECULAR; PLANT VIRUSES; REOVIRIDAE; SOFTWARE; VIRION;

EID: 34548008824     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-294-7:345     Document Type: Article

References (58)

1. Crowther, R. A., Amos, L. A., Finch, J. T., De Rosier, D. J., and Klug, A. (1970) Three dimensional reconstructions of spherical viruses by fourier synthesis from electron micrographs. Nature 226, 421-425.
2. Crowther, R. A. (1971) Procedures for three-dimensional reconstruction of spherical viruses by fourier synthesis from electron micrographs. Phil. Trans. Roy. Soc. Land. B. 261, 221-230.
3. Bottcher, B., Wynne, S. A., and Crowther, R. A. (1997) Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature 386, 88-91.
4. Conway, J. F., Cheng, N., Zlotnick, A., Wingfield, P. T., Stahl, S. J., and Steven, A. C. (1997) Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy. Nature 386, 91-94.
5. Zhou, Z. H., Dougherty, M., Jakana, J., He, J., Rixon, F. J., and Chiu, W. (2000) Seeing the herpesvirus capsid at 8.5 Å. Science 288, 877-880.
6. Zhou, Z. H., Baker, M. L., Jiang, W., Dougherty, M., Jakana, J., Dong, G., Lu, G., and Chiu, W. (2001) Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus. Nat. Struct. Biol. 8, 868-873.
7. Chiu, W., Baker, M. L., Jiang, W., Dougherty, M., and Schmid, M. F. (2005) Electron cryomicroscopy of biological machines at subnanometer resolution. Structure 13, 363-372.
8. Jiang, W., Baker, M. L., Ludtke, S. J., and Chiu, W. (2001) Bridging the information gap: computational tools for intermediate resolution structure interpretation. J. Mol. Biol. 308, 1033-1044.
9. Chiu, W., Baker, M. L., Jiang, W., and Zhou, Z. H. (2002) Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approaches. Curr. Opin. Struct. Biol. 12, 263-269.
10. Ludtke, S. J., Baldwin, P. R., and Chiu, W. (1999) EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128, 82-97.
11. Jiang, W., Li, Z., Zhang, Z., Booth, C. R., Baker, M. L., and Chiu, W. (2001) Semi-automated icosahedral particle reconstruction at sub-nanometer resolution. J. Struct. Biol. 136, 214-225.
12. Good, N. E., Winget, G. D., Winter, W., Connolly, T. N., Izawa, S., and Singh, R. M. (1966) Hydrogen ion buffers for biological research. Biochemistry 5, 467-477.
13. Adrian, M., Dubochet, J., Lepault, J., and McDowall, A. W. (1984) Cryo-electron microscopy of viruses. Nature 308, 32-36.
14. Dubochet, J., Adrian, M., Chang, J. J., et al. (1988) Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys. 21, 129-228.
15. Fukami, A. and Adachi, K. (1965) A new method of preparation of a self-perforated micro plastic grid and its application, J. Electron Microsc. 14, 112-118.
16. Jeng, T. W., Talmon, Y., and Chiu, W. (1988) Containment system for the preparation of vitrified-hydrated virus specimens. J. Electron Microsc. Tech. 8, 343-348.
17. Booth, C. R., Jiang, W., Baker, M. L., Zhou, Z. H., Ludtke, S. J., and Chiu, W. (2004) A 9 Åsingle particle reconstruction from CCD captured images on a 200 kV electron cryomicroscope. J. Struct. Biol. 147, 116-127.
18. Suloway, C., Pulokas, J., Fellmann, D., et al. (2005) Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151, 41-60.
19. Zhang, P., Beatty, A., Milne, J. L., and Subramaniam, S. (2001) Automated data collection with a Tecnai 12 electron microscope: applications for molecular imaging by cryomicroscopy. J. Struct. Biol. 135, 251-261.
20. Lei, J. and Frank, J. (2005) Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope. J. Struct. Biol. 150, 69-80.
21. Saban, S. D., Nepomuceno, R. R., Gritton, L. D., Nemerow, G. R., and Stewart, P. L. (2005) CryoEM structure at 9 Åresolution of an adenovirus vector targeted to hematopoietic cells. J. Mol. Biol. 349, 526-537.
22. Ludtke, S. J., Chen, D. H., Song, J. L., Chuang, D. T., and Chiu, W. (2004) Seeing GroEL at 6 Åresolution by single particle electron cryomicroscopy. Structure 12, 1129-1136.
23. Jiang, W., Baker, M. L., Wu, Q., Bajaj, C., and Chiu, W. (2003) Applications of a bilateral denoising filter in biological electron microscopy. J. Struct. Biol. 144, 114-122.
24. Zhu, Y., Carragher, B., Glaeser, R. M., et al. (2004) Automatic particle selection: results of a comparative study. J. Struct. Biol. 145, 3-14.
25. Kivioja, T., Ravantti, J., Verkhovsky, A., Ukkonen, E., and Bamford, D. (2000) Local average intensity-based method for identifying spherical particles in electron micrographs. J. Struct. Biol. 131, 126-134.
26. Thon, F. (1971) Phase contrast electron microscopy, in Electron Microscopy in Material Sciences (Valdré, U., ed.), Academic Press, New York, pp. 571-625.
27. Erickson, H. P. and Klug, A. (1971) Measurement and compensation of de-focusing and aberrations by Fourier processing of electron micrographs. Phil. Trans. Roy. Soc. Loud. B. 261, 105-118.
28. Hanszen, K. J. (1967) New knowledge on resolution and contrast in the electron microscope image. Naturwissenschaften 54, 125-133.
29. Saad, A., Ludtke, S. J., Jakana, J., Rixon, F. J., Tsuruta, H., and Chiu, W. (2001) Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination. J. Struct. Biol. 133, 32-42.
30. Frank, J., Radermacher, M., Penczek, P., et al. (1996) SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190-199.
31. van Heel, M., Harauz, G., Orlova, E. V., Schmidt, R., and Schatz, M. (1996) A new generation of the IMAGIC image processing system. J. Struct. Biol. 116, 17-24.
32. Grigorieff, N. (1998) Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 Åin ice. J. Mol. Biol. 277, 1033-1046.
33. Baker, T. S. and Cheng, R. H. (1996) A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy. J. Struct. Biol. 116, 120-130.
34. Sorzano, C. O., Marabini, R., Velazquez-Muriel, J., et al. (2004) XMIPP: a new generation of an open-source image processing package for electron microscopy. J. Struct. Biol. 148, 194-204.
35. Liang, Y., Ke, E. Y., and Zhou, Z. H. (2002) IMIRS: a high-resolution 3D reconstruction package integrated with a relational image database. J. Struct. Biol. 137, 292-304.
36. Jiang, W., Chang, J., Jakana, J., Weigele, P., King, J., and Chiu, W. (2006) Structure of Epsilon 15 phage reveals organization of genome and DNA packaging/injection apparatus. Nature 439, 612-616.
37. Harauz, G. and van Heel, M. (1986) Exact filters for general geometry three dimensional reconstruction. Optik 73, 146-156.
38. van Heel, M. and Schatz, M. (2005) Fourier shell correlation threshold criteria. J. Struct. Biol. 151, 250-262.
39. Rosenthal, P. B. and Henderson, R. (2003) Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721-745.
40. Baker, M. L., Jiang, W., Bowman, B. R., et al. (2003) Architecture of the herpes simplex virus major capsid protein derived from structural bioinformatics. J. Mol. Biol. 331, 447-456.
41. Jiang, W., Li, Z., Zhang, Z., Baker, M. L., Prevelige, P. E., Jr., and Chiu, W. (2003) Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions. Nat. Struct. Biol. 10, 131-135.
42. 365-385 1. Frank, J. (ed.) (1992) Electron Tomography: Three-Dimensional Imaging With the Transmission Electron Microscopy. Plenum Press, New York.
43. Zheng, S. Q., Braunfeld, B. M., Sedat, W. J., and Agard, A. D. (2004) An improved strategy for automated electron microscopic tomography. J. Struct, Biol. 147, 10-22.
44. Engelhardt, P. (2000) Electron tomography of chromosome structure, in Encyclopedia of Analytical Chemistry vol. 6 (Meyers, R. A., ed.), John Wiley & Sons Ltd, Chichester, pp. 4948-4984. Available at: http://www.lce.hut.fi/∼engelhar/. Accessed May 29, 2006.
45. IMOD (2005). Available at: URL: http://bio3d.colorado.edu/imod/. Accessed May 29, 2006.
46. Engelhardt, P., Meriläinen, J., Zhao, F., Uchiyama, S., Fukui, K., and Lehto, V.-P. (2006) Whole-mount immunoelectron tomography of chromosomes and cells, in Electron Microscopy Methods and Protocols, 2nd ed (Kuo, J., ed.), Humana, Totowa, NJ, pp. 387-405.
47. Brandt, S., Heikkonen, J., and Engelhardt, P. (2001) Multiphase method for automatic alignment of transmission electron microscope images using markers. J. Struct. Biol. 133, 10-22.
48. Brandt, S., Heikkonen, J., and Engelhardt, P. (2001) Automatic alignment of transmission electron microscope tilt-series without fiducial markers. J. Struct. Biol. 136, 201-213.
49. Brandt, S.S. and Ziese, U. (2006) Automatic TEM image alignment by trifocal geometry. J. Microsc. (Oxford) 222, 1-4.
50. Brandt, S.S. and Kolehmainen, V. (2004) Motion without correspondence from tomographic projections by Bayesian Inversion Theory, in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR 2004) Vol.1, Washington DC, pp. 582-587.
51. Brandt, S. S. (2006) Markerless alignment in electron tomography in Electron Tomography, 2nd ed. (Frank, J., ed.), Springer, New York, pp. 187-215.
52. BOB (2005) Available at: http://www.ahpcrc.org/software/bob/. Accessed May 30, 2006.
53. AnimaBob (2005) Available at: http://www.borg.umn.edu/~grant/AnimaBob/. Accessed May 30, 2006.
54. Chimera (2005) Available at: http://www.cgl.ucsf.edu/chimera/. Accessed May 30, 2006.
55. VMD (2005) Available at: http://www.ks.uiuc.edu/Research/vmd/. Accessed May 30, 2006.
56. SITUS (2005) Available at: http://situs.biomachina.org/. Accessed May 30, 2006.
57. Vis5D (2005) Available at: http://www.ssec.wisc.edu/∼billh/vis5d. html. Accessed May 30, 2006.
58. Sullivan, A. (2005) 3-Deep. IEEE Spectrum, INT. April 22-27.