Alignment of cryo-EM movies of individual particles by optimization of image translations

Journal of Structural Biology

Volumn 192, Issue 2, 2015, Pages 188-195

  Rubinstein, John L ^a,b,c   Brubaker, Marcus A ^c  

^a HOSPITAL FOR SICK CHILDREN   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

Algorithm; Beam induce motion; Cryo EM; DDD; Direct detector device; Direct electron detector; Local drift; Motion correction; Movie

Indexed keywords

ALGORITHM; ARTICLE; AUDIOVISUAL EQUIPMENT; BEAM INDUCED MOTION; CALCULATION; CAMERA; CONTROLLED STUDY; CRYOELECTRON MICROSCOPY; DIRECT DETECTOR DEVICE CAMERA; FOURIER TRANSFORMATION; IMAGE ANALYSIS; IMAGE PROCESSING; IMAGE QUALITY; IMAGE RECONSTRUCTION; IMAGE TRANSLATION; IMAGING AND DISPLAY; MATHEMATICAL COMPUTING; MICROSCOPE IMAGE; OPTICAL RESOLUTION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; ENZYMOLOGY; PROCEDURES; SACCHAROMYCES CEREVISIAE; THREE DIMENSIONAL IMAGING;

PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHMS; CRYOELECTRON MICROSCOPY; IMAGING, THREE-DIMENSIONAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; VACUOLAR PROTON-TRANSLOCATING ATPASES;

EID: 84946473054     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2015.08.007     Document Type: Article

References (15)

1. Baker L.A., Smith E.A., Bueler S.A., Rubinstein J.L. The resolution dependence of optimal exposures in liquid nitrogen temperature electron cryomicroscopy of catalase crystals. J. Struct. Biol. 2010, 169(3):431-437. 10.1016/j.jsb.2009.11.014.
2. Brilot A.F., Chen J.Z., Cheng A., Pan J., Harrison S.C., Potter C.S., Carragher B., Henderson R., Grigorieff N. Beam-induced motion of vitrified specimen on holey carbon film. J. Struct. Biol. 2012, 177(3):630-637. 10.1016/j.jsb.2012.02.003.
3. Byrd R.H., Lu P., Nocedal J., Zhu C. A limited memory algorithm for bound constrained optimization. SIAM J. Sci. Comput. 1995, 16(5):1190-1208.
4. Campbell M.G., Veesler D., Cheng A., Potter C.S., Carragher B. 2.8Å resolution reconstruction of the thermoplasma acidophilum 20S proteasome using cryo-electron microscopy. eLife 2015, 4:e06380.
5. Cao E., Liao M., Cheng Y., Julius D. TRPV1 structures in distinct conformations reveal activation mechanisms. Nature 2013, 504(7478):113-118. 10.1038/nature12823.
6. Glaeser R., McMullan G., Faruqi A., Henderson R. Images of paraffin monolayer crystals with perfect contrast: minimization of beam-induced specimen motion. Ultramicroscopy 2011, 111(2):90-100.
7. Grant T., Grigorieff N. Measuring the optimal exposure for single particle cryo-EM using a 2.6Å reconstruction of rotavirus VP6. eLife 2015, e06980.
8. Hayward S.B., Glaeser R.M. Radiation damage of purple membrane at low temperature. Ultramicroscopy 1979, 4(2):201-210.
9. Henderson R., Chen S., Chen J.Z., Grigorieff N., Passmore L.A., Ciccarelli L., Rubinstein J.L., Crowther R.A., Stewart P.L., Rosenthal P.B. Tilt-pair analysis of images from a range of different specimens in single-particle electron cryomicroscopy. J. Mol. Biol. 2011, 413(5):1028-1046. 10.1016/j.jmb.2011.09.008.
10. Liao M., Cao E., Julius D., Cheng Y. Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 2013, 504(7478):107-112. 10.1038/nature12822.
11. Li X., Mooney P., Zheng S., Booth C.R., Braunfeld M.B., Gubbens S., Agard D.A., Cheng Y. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 2013, 10(6):584-590. 10.1038/nmeth.2472.
12. McMullan G., Faruqi A. Electron microscope imaging of single particles using the medipix2 detector. Nucl. Instrum. Methods Phys. Res., Sect. A 2008, 591(1):129-133.
13. Scheres S.H.W. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 2012, 180(3):519-530. 10.1016/j.jsb.2012.09.006.
14. Scheres S.H. Beam-induced motion correction for sub-megadalton cryo-EM particles. eLife 2014, 3:e03665.
15. Unwin P.N.T., Henderson R. Molecular structure determination by electron microscopy of unstained crystalline specimens. J. Mol. Biol. 1975, 94(3):425-440.