A 9 Å single particle reconstruction from CCD captured images on a 200 kV electron cryomicroscope

Journal of Structural Biology

Volumn 147, Issue 2, 2004, Pages 116-127

  Booth, Christopher R ^a   Jiang, Wen ^a   Baker, Matthew L ^a   Zhou, Z Hong ^a,b   Ludtke, Steven J ^a   Chiu, Wah ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

Author keywords

CCD; Cryo EM; Cytoplasmic polyhedrosis virus; Electron cryomicroscopy; MTF; Structure

Indexed keywords

ARTICLE; CAMERA; CHARGE COUPLED DEVICE CAMERA; CONTROLLED STUDY; CRYOELECTRON MICROSCOPY; ELECTRON MICROSCOPE; FEASIBILITY STUDY; IMAGE PROCESSING; MATHEMATICAL COMPUTING; NONHUMAN; POLYHEDROSIS VIRUS; PRIORITY JOURNAL; RECORDING; VIRUS MORPHOLOGY; CHEMISTRY; EVALUATION; METHODOLOGY; REOVIRUS; THREE DIMENSIONAL IMAGING; ULTRASTRUCTURE; VIRION;

BOMBYX MORI CYPOVIRUS 1; CYPOVIRUS;

CRYOELECTRON MICROSCOPY; IMAGING, THREE-DIMENSIONAL; REOVIRIDAE; VIRION;

EID: 16644365074     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jsb.2004.02.004     Document Type: Article

References (33)

1. Aikens R., Agard D.A. Solid-state imagers for microscopy. Methods Cell Biol. 29:1989;291-313
2. Böttcher B., Wynne S.A., Crowther R.A. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature. 386:1997;88-91
3. Carragher B., Fellmann D., Guerra F., Milligan R.A., Mouche F., Pulokas J., Sheehan B., Quispe J., Suloway C., Zhu Y., Potter C.S. Rapid routine structure determination of macromolecular assemblies using electron microscopy: current progress and further challenges. J. Synchrotron. Radiat. 11:2004;83-85
4. Chiu W., Baker M.L., Jiang W., Zhou Z.H. Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approaches. Curr. Opin. Struct. Biol. 12:2002;263-269
5. Conway J.F., Cheng N., Zlotnick A., Wingfield P.T., Stahl S.J., Steven A.C. Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy. Nature. 386:1997;91-94
6. Crowther R.A. Procedures for three-dimensional reconstruction of spherical viruses by Fourier synthesis from electron micrographs. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 261:1971;221-230
7. de Ruijter W.J., Weiss J.K. Methods to measure properties of slow-scan CCD cameras for electron detection. Rev. Sci. Instrum. 63:1992;4314-4321
8. Dougherty M., Chiu W. Macromolecular structure visualization tools at NCMI. Microsc. Microanal. 6:2000;282-283
9. Downing K.H., Hendrickson F.M. Performance of a 2k CCD camera designed for electron crystallography at 400. kV Ultramicroscopy. 75:1999;215-233
10. Faruqi A.R., Subramaniam S. CCD detectors in high-resolution biological electron microscopy. Q. Rev. Biophys. 33:2000;1-27
11. Grimes J.M., Burroughs J.N., Gouet P., Diprose J.M., Malby R., Zientara S., Mertens P.P., Stuart D.I. The atomic structure of the bluetongue virus core. Nature. 395:1998;470-478
12. Ishizuka K. Analysis of electron image detection efficiency of slow-scan CCD cameras. Ultramicroscopy. 52:1993;7-20
13. Jiang W., Baker M.L., Ludtke S.J., Chiu W. Bridging the information gap: computational tools for intermediate resolution structure interpretation. J. Mol. Biol. 308:2001;1033-1044
14. Jiang W., Li Z., Zhang Z., Booth C.R., Baker M.L., Chiu W. Semi-automated icosahedral particle reconstruction at sub-nanometer resolution. J. Struct. Biol. 136:2001;214-225
15. Kivioja T., Ravantti J., Verkhovsky A., Ukkonen E., Bamford D. Local average intensity-based method for identifying spherical particles in electron micrographs. J. Struct. Biol. 131:2000;126-134
16. Kleywegt G.J., Jones T.A. Detecting folding motifs and similarities in protein structures. 1997;Academic Press, London
17. Ludtke S.J., Baldwin P.R., Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128:1999;82-97
18. Ludtke S.J., Jakana J., Song J.L., Chuang D.T., Chiu W. A 11.5. Å single particle reconstruction of GroEL using EMAN J. Mol. Biol. 314:2001;253-262
19. Ludtke S.J., Nason L., Tu H., Peng L., Chiu W. Object oriented database and electronic notebook for transmission electron microscopy. Microsc. Microanal. 9:2003;556-565
20. Meyer R.R., Kirkland A.I. Characterisation of the signal and noise transfer of CCD cameras for electron detection. Microsc. Res. Tech. 49:2000;269-280
21. Philippsen, A., 2003. Dino: Visualizing Structural Biology. Available from http://www.dino3d.org. 2003
22. Reinisch K.M., Nibert M.L., Harrison S.C. Structure of the reovirus core at 3.6. Å resolution Nature. 404:2000;960-967
23. Rouiller I., Pulokas J., Butel V.M., Milligan R.A., Wilson-Kubalek E.M., Potter C.S., Carragher B.O. Automated image acquisition for single-particle reconstruction using p97 as the biological sample. J. Struct. Biol. 133:2001;102-107
24. Saad A., Ludtke S.J., Jakana J., Rixon F.J., Tsuruta H., Chiu W. Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination. J. Struct. Biol. 133:2001;32-42
25. Sherman M.B., Brink J., Chiu W. Performance of a slow-scan CCD camera for macromolecular imaging in a 400. kV electron cryomicroscope Micron. 27:1996;129-139
26. Sherman M.B., Chiu W. Reliability of phases retrieved from 400-kV spot-scan images of purple membranes acquired on a slow-scan CCD camera. J. Microsc. 188(Pt 3):1997;285-289
27. Stewart P.L., Cary R.B., Peterson S.R., Chiu C.Y. Digitally collected cryo-electron micrographs for single particle reconstruction. Microsc. Res. Technol. 49:2000;224-232
28. Van Heel M. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy. 21:1987;111-123
29. van Zwet E.J., Zandbergen H.W. Measurement of the modulation transfer function for a slow-scan CCD camera on a TEM using a thin amorphous film as a test signal. Ultramicroscopy. 64:1996;49-55
30. Zhang P., Borgnia M.J., Mooney P., Shi D., Pan M., O'Herron P., Mao A., Brogan D., Milne J.L., Subramaniam S. Automated image acquisition and processing using a new generation of 4. k × 4 k CCD cameras for cryo electron microscopic studies of macromolecular assemblies J. Struct. Biol. 143:2003;135-144
31. Zhou Z.H., Chiu W. Determination of icosahedral viruse structure by electron cryomicroscopy at subnanometer resolution. Adv. Protein Chem. 64:2003;93-124
32. Zhou Z.H., Chiu W., Haskell K., Spears H. Jr., Jakana J., Rixon F.J., Scott L.R. Refinement of herpesvirus B-capsid structure on parallel supercomputers. Biophys. J. 74:1998;576-588
33. Zhou Z.H., Zhang H., Jakana J., Lu X.Y., Zhang J.Q. Cytoplasmic polyhedrosis virus structure at 8. A by electron cryomicroscopy: structural basis of capsid stability and mRNA processing regulation Structure (Camb). 11:2003;651-663