Methods to account for movement and flexibility in cryo-EM data processing

Methods

Volumn 100, Issue , 2016, Pages 35-41

  Rawson, S ^a   Iadanza, M G ^a   Ranson, N A ^a   Muench, S P ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

Cryo EM; Image processing; Motion correction; RELION

Indexed keywords

DYNEIN ADENOSINE TRIPHOSPHATASE; PEPTIDES AND PROTEINS; SPTP3 PROTEIN; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; CONTROLLED STUDY; CRYOELECTRON MICROSCOPY; IMAGE ANALYSIS; IMAGE PROCESSING; IMAGE QUALITY; IMAGE RECONSTRUCTION; IMAGING AND DISPLAY; MEASUREMENT ACCURACY; PRIORITY JOURNAL; SIGNAL NOISE RATIO; THREE DIMENSIONAL IMAGING; TWO DIMENSIONAL IMAGING; ALGORITHM; CHEMISTRY; COMPUTER SIMULATION; MACROMOLECULE; MOLECULAR MODEL; PROCEDURES; SOFTWARE; ULTRASTRUCTURE;

ALGORITHMS; COMPUTER SIMULATION; CRYOELECTRON MICROSCOPY; IMAGE PROCESSING, COMPUTER-ASSISTED; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; SOFTWARE;

EID: 84963958060     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2016.03.011     Document Type: Article

References (25)

1. Campbell M.G., Cheng A., Brilot A.F., Moeller A., Lyumkis D., Veesler D., et al. Movies of ice-embedded particles enhance resolution in electron cryo-microscopy. Structure 2012, 20:1823-1828. 10.1016/j.str.2012.08.026.
2. Bai X.C., Fernandez I.S., McMullan G., Scheres S.H. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles. eLife 2013, 2:e00461. 10.7554/eLife.00461.
3. Veesler D., Campbell M.G., Cheng A., Fu C.-Y., Murez Z., Johnson J.E., et al. Maximizing the potential of electron cryomicroscopy data collected using direct detectors. J. Struct. Biol. 2013, 184:193-202. 10.1016/j.jsb.2013.09.003.
4. Campbell M.G., Veesler D., Cheng A., Potter C.S., Carragher B. 2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy. eLife 2015, 4. 10.7554/eLife.06380.
5. Campbell M.G., Kearney B.M., Cheng A., Potter C.S., Johnson J.E., Carragher B., et al. Near-atomic resolution reconstructions using a mid-range electron microscope operated at 200 kV. J. Struct. Biol. 2014, 188:183-187. 10.1016/j.jsb.2014.09.008.
6. Bai X.-C., Yan C., Yang G., Lu P., Ma D., Sun L., et al. An atomic structure of human γ-secretase. Nature 2015, 525:212-217. 10.1038/nature14892.
7. Grant T., Grigorieff N. Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6. eLife 2015, 4:e06980. 10.7554/eLife.06980.
8. Paulsen C.E., Armache J.-P., Gao Y., Cheng Y., Julius D. Structure of the TRPA1 ion channel suggests regulatory mechanisms. Nature 2015, 520:511-517. 10.1038/nature14367.
9. Li X., Mooney P., Zheng S., Booth C.R., Braunfeld M.B., Gubbens S., et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 2013, 10:584-590. 10.1038/nmeth.2472.
10. Scheres S.H.W. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 2012, 180:519-530. 10.1016/j.jsb.2012.09.006.
11. Scheres S.H.W. Beam-induced motion correction for sub-megadalton cryo-EM particles. eLife 2014, 3. e03665.
12. Rubinstein J.L., Brubaker M.A. Alignment of cryo-EM movies of individual particles by optimization of image translations. J. Struct. Biol. 2015, 192:188-195. 10.1016/j.jsb.2015.08.007.
13. Ge J., Li W., Zhao Q., Li N., Chen M., Zhi P., et al. Architecture of the mammalian mechanosensitive Piezo1 channel. Nature 2015, 527:64-69. 10.1038/nature15247.
14. Scheres S.H.W. Semi-automated selection of cryo-EM particles in RELION-1.3. J. Struct. Biol. 2015, 189:114-122. 10.1016/j.jsb.2014.11.010.
15. Tang G., Peng L., Baldwin P.R., Mann D.S., Jiang W., Rees I., et al. EMAN2: An extensible image processing suite for electron microscopy. J. Struct. Biol. 2007, 157:38-46. 10.1016/j.jsb.2006.05.009.
16. Zhao J., Benlekbir S., Rubinstein J.L. Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase. Nature 2015, 521:241-245. 10.1038/nature14365.
17. Burgess S.A., Walker M.L., Thirumurugan K., Trinick J., Knight P.J. Use of negative stain and single-particle image processing to explore dynamic properties of flexible macromolecules. J. Struct. Biol. 2004, 147:247-258. 10.1016/j.jsb.2004.04.004.
18. Chowdhury S., Ketcham S.A., Schroer T.A., Lander G.C. Structural organization of the dynein-dynactin complex bound to microtubules. Nat. Struct. Mol. Biol. 2015, 22:345-347. 10.1038/nsmb.2996.
19. Radics J., Königsmaier L., Marlovits T.C. Structure of a pathogenic type 3 secretion system in action. Nature Publishing Group 2013, 21:82-87. 10.1038/nsmb.2722.
20. Lu P., Bai X.-C., Ma D., Xie T., Yan C., Sun L., et al. Three-dimensional structure of human γ-secretase. Nature 2014, 512:166-170. 10.1038/nature13567.
21. Song C.F., Papachristos K., Rawson S., Huss M., Wieczorek H., Paci E., et al. Flexibility within the rotor and stators of the vacuolar H+-ATPase. PLoS ONE 2013, 8:e82207. 10.1371/journal.pone.0082207.
22. Richardson R.A., Papachristos K., Read D.J., Harlen O.G., Harrison M., Paci E., et al. Understanding the apparent stator-rotor connections in the rotary ATPase family using coarse-grained computer modeling. Proteins 2014, 82:3298-3311. 10.1002/prot.24680.
23. Stewart A.G., Lee L.K., Donohoe M., Chaston J.J., Stock D. The dynamic stator stalk of rotary ATPases. Nat. Commun. 2012, 3:687. 10.1038/ncomms1693.
24. Rawson S., Phillips C., Huss M., Tiburcy F., Wieczorek H., Trinick J., et al. Structure of the vacuolar H(+)-ATPase rotary motor reveals new mechanistic insights. Structure 2015, 23:461-471. 10.1016/j.str.2014.12.016.
25. Kucukelbir A., Sigworth F.J., Tagare H.D. Quantifying the local resolution of cryo-EM density maps. Nat. Methods 2013, 11:63-65. 10.1038/nmeth.2727.