A test-bed for optimizing high-resolution single particle reconstructions

Journal of Structural Biology

Volumn 163, Issue 1, 2008, Pages 29-39

  Stagg, Scott M ^a,b   Lander, Gabriel C ^a   Quispe, Joel ^a   Voss, Neil R ^a   Cheng, Anchi ^a   Bradlow, Henry ^a   Bradlow, Steven ^c   Carragher, Bridget ^a   Potter, Clinton S ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Automation; CryoEM; Database; Optimization; Single particle reconstruction; TEM

Indexed keywords

ARTICLE; CRYOELECTRON MICROSCOPY; DATA ANALYSIS; ELECTRON BEAM; PARTICLE SIZE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; SIGNAL NOISE RATIO; X RAY CRYSTALLOGRAPHY;

CRYOELECTRON MICROSCOPY; GROEL PROTEIN; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; INFORMATION STORAGE AND RETRIEVAL; LABORATORY TECHNIQUES AND PROCEDURES; PROTEINS; RESEARCH DESIGN;

EID: 45549102308     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2008.04.005     Document Type: Article

References (33)

1. Baker M.L., Ju T., and Chiu W. Identification of secondary structure elements in intermediate-resolution density maps. Structure 15 (2007) 7-19
2. Borgnia M.J., Shi D., Zhang P., and Milne J.L. Visualization of alpha-helical features in a density map constructed using 9 molecular images of the 1.8 MDa icosahedral core of pyruvate dehydrogenase. J. Struct. Biol. 147 (2004) 136-145
3. Bottcher B., Wynne S.A., and Crowther R.A. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature 386 (1997) 88-91
4. Braig K., Adams P.D., and Brunger A.T. Conformational variability in the refined structure of the chaperonin GroEL at 2.8 Å resolution. Nat. Struct. Biol. 2 (1995) 1083-1094
5. Chen J.Z., Sachse C., Xu C., Mielke T., Spahn C.M., and Grigorieff N. A dose-rate effect in single-particle electron microscopy. J. Struct. Biol. 161 (2008) 92-100
6. Conway J.F., Cheng N., Zlotnick A., Wingfield P.T., Stahl S.J., and Steven A.C. Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy. Nature 386 (1997) 91-94
7. Fellmann D., Pulokas J., Milligan R.A., Carragher B., and Potter C.S. A relational database for cryoEM: experience at one year and 50 000 images. J. Struct. Biol. 137 (2002) 273-282
8. Gabashvili I.S., Agrawal R.K., Spahn C.M.T., Grassucci R.A., Svergun D.I., Frank J., and Penczek P. Solution structure of the E. Coli 70S ribosome at 11.5 Å resolution. Cell 100 (2000) 537-549
9. Glaeser R.M. Review: electron crystallography: present excitement, a nod to the past, anticipating the future. J. Struct. Biol. 128 (1999) 3-14
10. Glaeser R.M. Historical background: why is it important to improve automated particle selection methods?. J. Struct. Biol. 145 (2004) 15-18
11. Gonen T., Cheng Y., Sliz P., Hiroaki Y., Fujiyoshi Y., Harrison S.C., and Walz T. Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature 438 (2005) 633-638
12. Harauz G., and Van Heel M. Exact filters for general geometry three dimensional reconstruction. Optik 73 (1986) 146-156
13. Henderson R. The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules. Q. Rev. Biophys. 28 (1995) 171-193
14. Liu X., Jiang W., Jakana J., and Chiu W. Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. J. Struct. Biol. 160 (2007) 11-27
15. Ludtke S.J., Baldwin P.R., and Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128 (1999) 82-97
16. Ludtke S.J., Chen D.H., Song J.L., Chuang D.T., and Chiu W. Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy. Structure (Camb.) 12 (2004) 1129-1136
17. Mallick S.P., Carragher B., Potter C.S., and Kriegman D.J. ACE: automated CTF estimation. Ultramicroscopy 104 (2005) 8-29
18. Mooney P. Optimization of image collection for cellular electron microscopy. Methods Cell Biol. 79 (2007) 661-719
19. Orlova E.V., Dube P., Harris J.R., Beckmann E., Zemlin F., Markl J., and van Heel M. Structure of Keyhole Limpet Hemocyanin Type 1 (KLH1) at 15 Å resolution by electron cryomicroscopy and angular reconstitution. J. Mol. Biol. 1997 (1997) 417-437
20. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., and Ferrin T.E. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25 (2004) 1605-1612
21. Ranson N.A., Clare D.K., Farr G.W., Houldershaw D., Horwich A.L., and Saibil H.R. Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes. Nat. Struct. Mol. Biol. 13 (2006) 147-152
22. Ranson N.A., Farr G.W., Roseman A.M., Gowen B., Fenton W.A., Horwich A.L., and Saibil H.R. ATP-bound states of GroEL captured by cryo-electron microscopy. Cell 107 (2001) 869-879
23. Roseman A.M. Particle finding in electron micrographs using a fast local correlation algorithm. Ultramicroscopy 94 (2003) 225-236
24. Rosenthal P.B., and Henderson R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333 (2003) 721-745
25. Sander B., Golas M.M., and Stark H. Advantages of CCD detectors for de novo three-dimensional structure determination in single-particle electron microscopy. J. Struct. Biol. 151 (2005) 92-105
26. Saxon W.O., and Baumeister W. The correlation averaging of a regularly arranged bacterial cell envelope protein. J. Microsc. 127 (1982) 127-138
27. Sigler P.B., Xu Z., Rye H.S., Burston S.G., Fenton W.A., and Horwich A.L. Structure and function in GroEL-mediated protein folding. Annu. Rev. Biochem. 67 (1998) 581-608
28. Sousa D., and Grigorieff N. Ab initio resolution measurement for single particle structures. J. Struct. Biol. 157 (2007) 201-210
29. Stagg S.M., Lander G.C., Pulokas J., Fellmann D., Cheng A., Quispe J.D., Mallick S.P., Avila R.M., Carragher B., and Potter C.S. Automated cryoEM data acquisition and analysis of 284742 particles of GroEL. J. Struct. Biol. 155 (2006) 470-481
30. Stewart A., and Grigorieff N. Noise bias in the refinement of structures derived from single particles. Ultramicroscopy 102 (2004) 67-84
31. Suloway C., Pulokas J., Fellmann D., Cheng A., Guerra F., Quispe J., Stagg S., Potter C.S., and Carragher B. Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151 (2005) 41-60
32. van Heel M., and Schatz M. Fourier shell correlation threshold criteria. J. Struct. Biol. 151 (2005) 250-262
33. Zhang X., Settembre E., Xu C., Dormitzer P.R., Bellamy R., Harrison S.C., and Grigorieff N. Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proc. Natl. Acad. Sci. USA 105 (2008) 1867-1872