Automatic lattice determination for two-dimensional crystal images

Journal of Structural Biology

Volumn 160, Issue 3, 2007, Pages 353-361

  Zeng, Xiangyan ^a   Gipson, Bryant ^a   Zheng, Zi Yan ^a   Renault, Ludovic ^a   Stahlberg, Henning ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

2D membrane protein crystals; Computer image processing; Electron crystallography; Lattice determination

Indexed keywords

MEMBRANE PROTEIN;

ARTICLE; AUTOMATION; CALCULATION; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; FOURIER TRANSFORMATION; GEOMETRY; IMAGE ANALYSIS; IMAGE PROCESSING; INFORMATION PROCESSING; PRIORITY JOURNAL; PROTEIN STRUCTURE; X RAY DIFFRACTION;

ALGORITHMS; CRYSTALLIZATION; CRYSTALLOGRAPHY; FOURIER ANALYSIS; IMAGE PROCESSING, COMPUTER-ASSISTED; MEMBRANE PROTEINS; MICROSCOPY, ELECTRON, TRANSMISSION; SOFTWARE;

EID: 36048969226     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2007.08.008     Document Type: Article

References (34)

1. Amos L.A., Henderson R., and Unwin P.N. Three-dimensional structure determination by electron microscopy of two-dimensional crystals. Prog. Biophys. Mol. Biol. 39 (1982) 183-231
2. Crowther R.A., Henderson R., and Smith J.M. MRC image processing programs. J. Struct. Biol. 116 (1996) 9-16
3. Gipson B., Zeng X., Zhang Z.Y., and Stahlberg H. 2dx-user-friendly image processing for 2D crystals. J. Struct. Biol. 157 (2007) 64-72
4. 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
5. Gonen T., Sliz P., Kistler J., Cheng Y., and Walz T. Aquaporin-0 membrane junctions reveal the structure of a closed water pore. Nature 429 (2004) 193-197
6. Grigorieff N., Ceska T.A., Downing K.H., Baldwin J.M., and Henderson R. Electron-crystallographic refinement of the structure of bacteriorhodopsin. J. Mol. Biol. 259 (1996) 393-421
7. Henderson R., Baldwin J.M., Ceska T.A., Zemlin F., Beckmann E., and Downing K.H. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J. Mol. Biol. 213 (1990) 899-929
8. Henderson R., and Unwin P.N. Three-dimensional model of purple membrane obtained by electron microscopy. Nature 257 (1975) 28-32
9. Higashi T. Auto-indexing of oscillation images. J. Appl. Cryst. 23 (1990) 253-257
10. Hirai T., Heymann J.A., Shi D., Sarker R., Maloney P.C., and Subramaniam S. Three-dimensional structure of a bacterial oxalate transporter. Nat. Struct. Biol. 9 (2002) 597-600
11. Hiroaki Y., Tani K., Kamegawa A., Gyobu N., Nishikawa K., Suzuki H., Walz T., Sasaki S., Mitsuoka K., Kimura K., Mizoguchi A., and Fujiyoshi Y. Implications of the aquaporin-4 structure on array formation and cell adhesion. J. Mol. Biol. 355 (2006) 628-639
12. Holm P.J., Bhakat P., Jegerschold C., Gyobu N., Mitsuoka K., Fujiyoshi Y., Morgenstern R., and Hebert H. Structural basis for detoxification and oxidative stress protection in membranes. J. Mol. Biol. 360 (2006) 934-945
13. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 26 (1993) 795-800
14. Kabsch W. Automatic processing of rotation diffraction patterns. J. Appl. Cryst. 21 (1988) 67-71
15. Kim S. Auto-indexing oscillation photographs. J. Appl. Cryst. 22 (1989) 53-60
16. Kühlbrandt W., Wang D.N., and Fujiyoshi Y. Atomic model of plant light-harvesting complex by electron crystallography. Nature 367 (1994) 614-621
17. Kukulski W., Schenk A.D., Johanson U., Braun T., de Groot B.L., Fotiadis D., Kjellbom P., and Engel A. The 5 Å structure of heterologously expressed plant aquaporin SoPIP2;1. J. Mol. Biol. 350 (2005) 611-616
18. Leslie A.G. The integration of macromolecular diffraction data. Acta Cryst. D Biol. Crystallogr. 62 (2006) 48-57
19. Leslie A.G.W. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EAMCB News-letter Prot. Cryst. 26 (1992) 22-33
20. Miyazawa A., Fujiyoshi Y., and Unwin N. Structure and gating mechanism of the acetylcholine receptor pore. Nature 424 (2003) 949-955
21. Murata K., Mitsuoka K., Hirai T., Walz T., Agre P., Heymann J.B., Engel A., and Fujiyoshi Y. Structural determinants of water permeation through aquaporin-1. Nature 407 (2000) 599-605
22. Nogales E., Wolf S.G., and Downing K.H. Structure of the alpha beta tubulin dimer by electron crystallography. Nature 391 (1998) 199-203
23. Otwinowski Z.M., and Minor W. DENZO and SCALEPACK. In: Rossmann M.G., and Arnold E. (Eds). International tables for crystallography. Crystallography of biological macromolecules Vol. F (2001), Kluwer Academic Publishers., Dordrecht, The Netherlands 226-235
24. Otwinowski Z.M., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Meth. Enzymol. 276 (1997) 307-326
25. Pflugrath J.W. The finer things in X-ray diffraction data collection. Acta Cryst. D Biol. Crystallogr. 55 (1999) 1718-1725
26. Ren G., Reddy V.S., Cheng A., Melnyk P., and Mitra A.K. Visualization of a water-selective pore by electron crystallography in vitreous ice. Proc. Natl. Acad. Sci. USA 98 (2001) 1398-1403
27. Rossmann M.G., and van Beek C.G. Data processing. Acta Cryst. D Biol. Crystallogr. 55 (1999) 1631-1640
28. Schenk A.D., Werten P.J., Scheuring S., de Groot B.L., Müller S.A., Stahlberg H., Philippsen A., and Engel A. The 4.5 A structure of human AQP2. J. Mol. Biol. 350 (2005) 278-289
29. Shaw P.J., and Hills G.J. Tilted specimen in the electron microscope: A simple specimen holder and the calculation of tilt angles for crystalline specimens. Micron 12 (1981) 279-282
30. Smith J.M. Ximdisp-A visualization tool to aid structure determination from electron microscope images. J. Struct. Biol. 125 (1999) 223-228
31. Steller I., Bolotovsky R., and Rossmann M.G. An algorithm for automatic indexing of oscillation images using Fourier analysis. J. Appl. Cryst. 30 (1997) 1036-1040
32. Tate C.G., Ubarretxena-Belandia I., and Baldwin J.M. Conformational changes in the multidrug transporter EmrE associated with substrate binding. J. Mol. Biol. 332 (2003) 229-242
33. Valpuesta J.M., Carrascosa J.L., and Henderson R. Analysis of electron microscope images and electron diffraction patterns of thin crystals of phi 29 connectors in ice. J. Mol. Biol. 240 (1994) 281-287
34. Vinothkumar K.R., Smits S.H., and Kühlbrandt W. pH-induced structural change in a sodium/proton antiporter from Methanococcus jannaschii. EMBO J. 24 (2005) 2720-2729