De novo protein structure determination from near-atomic-resolution cryo-EM maps

Nature Methods

Volumn 12, Issue 4, 2015, Pages 335-338

  Wang, Ray Yu Ruei ^a,b   Kudryashev, Mikhail ^c   Li, Xueming ^d,f   Egelman, Edward H ^e   Basler, Marek ^c   Cheng, Yifan ^d   Baker, David ^a,b   Dimaio, Frank ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF BASEL   (Switzerland)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF VIRGINIA   (United States)

^f TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL ANALYSIS; CRYOELECTRON MICROSCOPY; DENSITY; MODEL; MONTE CARLO METHOD; NEAR ATOMIC RESOLUTION DENSITY CRYOELECTRON MICROSCOPY MAP; NONHUMAN; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN STRUCTURE; TYPE VI SECRETION SYSTEM; VIBRIO CHOLERAE; X RAY CRYSTALLOGRAPHY; CHEMICAL STRUCTURE; CHEMISTRY; PHYSICAL CHEMISTRY; PROCEDURES; PROTEIN CONFORMATION; TIME FACTOR;

PROTEIN;

CHEMISTRY, PHYSICAL; CRYOELECTRON MICROSCOPY; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN CONFORMATION; PROTEINS; TIME FACTORS;

EID: 84926516252     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.3287     Document Type: Article

References (29)

1. Hryc, C.F., Chen, D.H. & Chiu, W. Curr. Opin. Virol. 1, 110-117 (2011).
2. Liao, M., Cao, E., Julius, D. & Cheng, Y. Nature 504, 107-112 (2013).
3. Bai, X.C., Fernandez, I.S., McMullan, G. & Scheres, S.H. eLife 2, e00461 (2013).
4. Lu, P. et al. Nature 512, 166-170 (2014).
5. Rossmann, M.G., Bernal, R. & Pletnev, S.V. J. Struct. Biol. 136, 190-200 (2001).
6. DiMaio, F. et al. Nat. Methods doi:10.1038/nmeth.3286 (23 February 2015).
7. Allegretti, M., Mills, D.J., McMullan, G., Kühlbrandt, W. & Vonck, J. eLife 3, e01963 (2014).
8. Amunts, A. et al. Science 343, 1485-1489 (2014).
9. Cowtan, K. Acta Crystallogr. D Biol. Crystallogr. 62, 1002-1011 (2006).
10. Terwilliger, T.C. et al. Acta Crystallogr. D Biol. Crystallogr. 64, 61-69 (2008).
11. Baker, M.R., Rees, I., Ludtke, S.J., Chiu, W. & Baker, M.L. Structure 20, 450-463 (2012).
12. Lindert, S. et al. Structure 17, 990-1003 (2009).
13. Gront, D., Kulp, D.W., Vernon, R.M., Strauss, C.E. & Baker, D. PLoS ONE 6, e23294 (2011).
14. Song, Y. et al. Structure 21, 1735-1742 (2013).
15. Kudryashev, M. et al. Cell doi:10.1016/j.cell.2015.01.037 (in the press).
16. Bradley, P., Misura, K.M. & Baker, D. Science 309, 1868-1871 (2005).
17. Raman, S. et al. Science 327, 1014-1018 (2010).
18. DiMaio, F.P., Soni, A.B., Phillips, G.N. Jr. & Shavlik, J.W. Int. J. Data Min. Bioinform. 3, 205-227 (2009).
19. DiMaio, F., Tyka, M.D., Baker, M.L., Chiu, W. & Baker, D. J. Mol. Biol. 392, 181-190 (2009).
20. Adams, P.D. et al. Acta Crystallogr. D Biol. Crystallogr. 66, 213-221 (2010).
21. Winn, M.D. et al. Acta Crystallogr. D Biol. Crystallogr. 67, 235-242 (2011).
22. Chen, X., Wang, Q., Ni, F. & Ma, J. Proc. Natl. Acad. Sci. USA 107, 11352-11357 (2010).
23. Mindell, J.A. & Grigorieff, N. J. Struct. Biol. 142, 334-347 (2003).
24. Roseman, A.M. J. Struct. Biol. 145, 91-99 (2004).
25. Frank, J. et al. J. Struct. Biol. 116, 190-199 (1996).
26. Li, X., Grigorieff, N. & Cheng, Y. J. Struct. Biol. 172, 407-412 (2010).
27. Li, X. et al. Nat. Methods 10, 584-590 (2013).
28. Scheres, S.H. & Chen, S. Nat. Methods 9, 853-854 (2012).
29. Rosenthal, P.B. & Henderson, R. J. Mol. Biol. 333, 721-745 (2003).