Hostname: page-component-cd9895bd7-7cvxr Total loading time: 0 Render date: 2024-12-28T03:01:35.844Z Has data issue: false hasContentIssue false

Electron Digital Imaging toward High-Resolution Structure Analysis of Biological Macromolecules

Published online by Cambridge University Press:  04 July 2008

Saori Maki-Yonekura
Affiliation:
The W. M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158-2532, USA
Koji Yonekura*
Affiliation:
The W. M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158-2532, USA
*
Corresponding author. E-mail: yone@spring8.or.jp
Get access

Abstract

Digital imaging has been applied to structure analysis of biological macromolecules in combination with electron energy filtering. Energy filtering can improve the image contrast of frozen-hydrated specimens, but needs a high-sensitivity imaging device instead of photographic film, because of a decrease in electrons after filtration. Here, a lens-coupled slow-scan charge-coupled device (SSCCD) camera with a post-column-type energy filter were examined to image bacterial flagellar filaments embedded in ice. We first measured the modulation transfer function of this camera and showed the remarkable improvement, compared to other fiber-coupled SSCCD cameras. The 3D structure calculated at ∼7-Å resolution clearly resolves α-helices. Furthermore, filtered datasets recorded on the SSCCD camera with liquid-nitrogen and liquid-helium cooling were compared with the previous unfiltered one on film with liquid-helium cooling. This report describes the suitability of digital imaging with energy filtering for higher-resolution structure studies from its practical application.

Type
Biological Applications
Copyright
Copyright © Microscopy Society of America 2008

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

Booth, C.R., Jakana, J. & Chiu, W. (2006). Assessing the capabilities of a 4kx4k CCD camera for electron cryo-microscopy at 300 kV. J Struct Biol 156, 556563.CrossRefGoogle Scholar
Booth, C.R., Jiang, W., Baker, M.L., Zhou, Z.H., Ludtke, S.J. & Chiu, W. (2004). A 9 Å single particle reconstruction from CCD captured images on a 200 kV electron cryomicroscope. J Struct Biol 147, 116127.CrossRefGoogle ScholarPubMed
Comolli, L.R. & Downing, K.H. (2005). Dose tolerance at helium and nitrogen temperatures for whole cell electron tomography. J Struct Biol 152, 149156.CrossRefGoogle ScholarPubMed
de Ruijter, W.J. & Weiss, J.K. (1992). Methods to measure properties of slow-scan CCD cameras for electron detection. Rev Sci Instrum 63, 43144321.CrossRefGoogle Scholar
Faruqi, A.R. & Henderson, R. (2007). Electronic detectors for electron microscopy. Curr Opin Struct Biol 17, 549555.CrossRefGoogle ScholarPubMed
Fujiyoshi, Y. (1998). The structural study of membrane proteins by electron crystallography. Adv Biophys 35, 2580.CrossRefGoogle ScholarPubMed
Henderson, R. (2004). Realizing the potential of electron cryo-microscopy. Q Rev Biophys 37, 313.CrossRefGoogle ScholarPubMed
Iancu, C.V., Wright, E.R., Heymann, J.B. & Jensen, G.J. (2006). A comparison of liquid nitrogen and liquid helium as cryogens for electron cryotomography. J Struct Biol 153, 231240.CrossRefGoogle ScholarPubMed
Langmore, J.P. & Smith, M.F. (1992). Quantitative energy-filtered electron microscopy of biological molecules in ice. Ultramicroscopy 46, 349373.CrossRefGoogle ScholarPubMed
Ludtke, S.J., Serysheva, I.I., Hamilton, S.L. & Chiu, W. (2005). The pore structure of the closed RyR1 channel. Structure 13, 12031211.CrossRefGoogle ScholarPubMed
Maki-Yonekura, S., Yonekura, K. & Namba, K. (2003). Domain movements of HAP2 in the cap-filament complex formation and growth process of the bacterial flagellum. Proc Natl Acad Sci USA 100, 1552815533.CrossRefGoogle ScholarPubMed
McMullan, G., Cattermole, D.M., Chen, S., Henderson, R., Llopart, X., Summerfield, C., Tlustos, L. & Faruqi, A.R. (2007). Electron imaging with Medipix2 hybrid pixel detector. Ultramicroscopy 107, 401413.CrossRefGoogle ScholarPubMed
McRee, D.E. (1999). XtalView/Xfit—A versatile program for manipulating atomic coordinates and electron density. J Struct Biol 125, 156165.CrossRefGoogle ScholarPubMed
Meyer, R.R., Kirkland, A.I., Dunin-Borkowski, R.E. & Hutchison, J.L. (2000). Experimental characterisation of CCD cameras for HREM at 300 kV. Ultramicroscopy 85, 913.CrossRefGoogle Scholar
Mimori, Y., Yamashita, I., Murata, K., Fujiyoshi, Y., Yonekura, K., Toyoshima, C. & Namba, K. (1995). The structure of the R-type straight flagellar filament of Salmonella at 9 Å resolution by electron cryomicroscopy. J Mol Biol 249, 6987.CrossRefGoogle ScholarPubMed
Miyazawa, A., Fujiyoshi, Y., Stowell, M. & Unwin, N. (1999). Nicotinic acetylcholine receptor at 4.6 Å resolution: Transverse tunnels in the channel wall. J Mol Biol 288, 765786.CrossRefGoogle ScholarPubMed
Mooney, P. (2007). Optimization of image collection for cellular electron microscopy. Methods Cell Biol 79, 661719.CrossRefGoogle ScholarPubMed
Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C. & Ferrin, T.E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. J Comput Chem 25, 16051612.CrossRefGoogle ScholarPubMed
Sander, B., Golas, M.M. & Stark, H. (2005). Advantages of CCD detectors for de novo three-dimensional structure determination in single-particle electron microscopy. J Struct Biol 151, 92105.CrossRefGoogle Scholar
Schröder, R.R., Hofmann, W. & Ménétret, J.-F. (1990). Zero-loss energy filtering as improved imaging mode in cryoelectronmicroscopy of frozen-hydrated specimens. J Struct Biol 105, 2834.CrossRefGoogle Scholar
Stagg, S.M., Lander, G.C., Pulokas, J., Fellmann, D., Cheng, A., Quispe, J.D., Mallick, S.P., Avila, R.M., Carragher, B. & Potter, C.S. (2006). Automated cryoEM data acquisition and analysis of 284742 particles of GroEL. J Struct Biol 155, 470481.CrossRefGoogle ScholarPubMed
Yonekura, K., Braunfeld, M.B., Maki-Yonekura, S. & Agard, D.A. (2006). Electron energy filtering significantly improves amplitude contrast of frozen-hydrated protein at 300 kV. J Struct Biol 156, 524536.CrossRefGoogle Scholar
Yonekura, K., Maki-Yonekura, S. & Namba, K. (2002). Quantitative comparison of zero-loss and conventional electron diffraction from 2D and thin 3D protein crystals. Biophys J 82, 27842797.CrossRefGoogle ScholarPubMed
Yonekura, K., Maki-Yonekura, S. & Namba, K. (2003a). Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Nature 424, 643650.CrossRefGoogle ScholarPubMed
Yonekura, K., Maki-Yonekura, S. & Namba, K. (2005). Building the atomic model for the bacterial flagellar filament by electron cryomicroscopy and image analysis. Structure 13, 407412.CrossRefGoogle ScholarPubMed
Yonekura, K. & Toyoshima, C. (2000). Structure determination of tubular crystals of membrane proteins. III. Solvent flattening. Ultramicroscopy 84, 2945.CrossRefGoogle ScholarPubMed
Yonekura, K. & Toyoshima, C. (2007). Structure determination of tubular crystals of membrane proteins. IV. Distortion correction and its combined application with real-space averaging and solvent flattening. Ultramicroscopy 107, 11411158.CrossRefGoogle ScholarPubMed
Yonekura, K., Toyoshima, C., Maki-Yonekura, S. & Namba, K. (2003b). GUI programs for processing individual images in early stages of helical image reconstruction—For high-resolution structure analysis. J Struct Biol 144, 184194.CrossRefGoogle ScholarPubMed
Zhu, J., Penczek, P.A., Schröder, R. & Frank, J. (1997). Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: Procedure and application to the 70S Escherichia coli ribosome. J Struct Biol 118, 197219.CrossRefGoogle Scholar