Application of the iterative helical real-space reconstruction method to large membranous tubular crystals of P-type ATPases

Journal of Structural Biology

Volumn 157, Issue 1, 2007, Pages 106-116

  Pomfret, Andrew J ^a   Rice, William J ^b   Stokes, David L ^a,b  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NEW YORK STRUCTURAL BIOLOGY CENTER   (United States)

Author keywords

Electron microscopy; Helical reconstruction; Image analysis; Iterative helical real space reconstruction; Tubular crystals

Indexed keywords

ADENOSINE TRIPHOSPHATASE (CALCIUM); ADENOSINE TRIPHOSPHATASE (POTASSIUM SODIUM); CALCIUM CHANNEL P TYPE;

ALGORITHM; ARTICLE; CONTRAST ENHANCEMENT; CRYSTAL STRUCTURE; ENZYME STRUCTURE; FOURIER ANALYSIS; IMAGE ANALYSIS; IMAGE QUALITY; IMAGE RECONSTRUCTION; ITERATIVE HELICAL REAL SPACE RECONSTRUCTION; NONHUMAN; PARTICLE SIZE; PRIORITY JOURNAL; RABBIT; SIGNAL NOISE RATIO; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

ANIMALS; CALCIUM CHANNELS, P-TYPE; COMPUTATIONAL BIOLOGY; CRYSTALLIZATION; IMAGE PROCESSING, COMPUTER-ASSISTED; MEMBRANE PROTEINS; MICROSCOPY, ELECTRON; MODELS, MOLECULAR; NA(+)-K(+)-EXCHANGING ATPASE; PECTINIDAE; RABBITS;

ORYCTOLAGUS CUNICULUS;

EID: 33845305824     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2006.05.012     Document Type: Article

References (32)

1. Beroukhim R., and Unwin N. Distortion correction of tubular crystals: improvements in the acetylcholine receptor structure. Ultramicroscopy 70 (1997) 57-81
2. Castellani L., Hardwicke P.M., et al. Dimer ribbons in the three-dimensional structure of sarcoplasmic reticulum. J. Mol. Biol. 185 (1985) 579-594
3. Crowther R.A., DeRosier D.J., et al. The reconstitution of a three-dimensional stucture from projections and its application to electron microscopy. Proc. Roy. Soc. Lond. 317 (1970) 319-340
4. Crowther R.A., Henderson R., et al. MRC image processing programs. J. Struct. Biol. 116 (1996) 9-16
5. DeRosier D.J., and Klug A. Reconstruction of three dimensional structures from electron micrographs. Nature 217 (1968) 130-134
6. DeRosier D.J., and Moore P.B. Reconstruction of three-dimensional images from electron micrographs of structures with helical symmetry. J. Mol. Biol. 52 (1970) 355-369
7. DeRosier D., Stokes D.L., et al. Averaging data derived from images of helical structures with different symmetries. J. Mol. Biol. 289 (1999) 159-165
8. Egelman E.H. An algorithm for straightening images of curved filamentous structures. Ultramicroscopy 19 (1986) 367-374
9. Egelman E.H. A robust algorithm for the reconstruction of helical filaments using single-particle methods. Ultramicroscopy 85 (2000) 225-234
10. Erickson H.P., and Klug A. Measurement and compensation of defocusing and aberrations by fourier processing of electron micrographs. Phil. Trans. Roy. Soc. Lond. 261 (1971) 105-118
11. Frank J., Radermacher M., et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116 (1996) 190-199
12. Galkin V.E., Orlova A., et al. Do the utrophin tandem calponin homology domains bind F-actin in a compact or extended conformation?. J. Mol. Biol. 331 (2003) 967-972
13. Henderson R., Baldwin J.M., et al. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J. Mol. Biol. 213 (1990) 899-929
14. Henderson R., and Unwin P.N.T. Three-dimensional model of purple membrane obtained from electron microscopy. Nature 257 (1975) 28-32
15. Jiang W., and Ludtke S.J. Electron cryomicroscopy of single particles at subnanometer resolution. Curr. Opin. Struct. Biol. 15 (2005) 571-577
16. Klug A. From macromolecules to biological assemblies. Nobel Lecture, 8 December 1982. Biosci. Rep. 3 (1983) 395-430
17. Klug A., Crick F.H.C., et al. Diffraction by helical structures. Acta Crystallogr. 11 (1958) 199-213
18. Morgan D.G., and DeRosier D. Processing images of helical structures: a new twist. Ultramicroscopy 46 (1992) 263-285
19. Mu X.Q., Egelman E.H., et al. Structure and function of Hib pili from Haemophilus influenzae type b. J. Bacteriol. 184 (2002) 4868-4874
20. Penczek P., Zhu J., et al. 3D reconstruction with contrast transfer compensation from defocus series. Scanning Micros. 11 (1997) 147-154
21. 2 states. Biophys. J. 80 (2001) 2187-2197
22. 2+-ATPase. J. Biol. Chem. 280 (2005) 18063-18072
23. Stokes D.L., Zhang P., et al. Cryoelectron microscopy of the calcium pump from sarcoplasmic reticulum: two crystal forms reveal two different conformations. Acta Physiol. Scand. Suppl. 643 (1998) 35-43
24. Toyoshima C., Sasabe H., et al. Three-dimensional cryo-electron microscopy of the calcium ion pump in the sarcoplasmic reticulum membrane. Nature 362 (1993) 469-471
25. Toyoshima C., and Unwin N. Three-dimensional structure of the acetylcholine receptor by cryoelectron microscopy and helical image reconstruction. J. Cell. Biol. 111 (1990) 2623-2635
26. Unwin N. Refined structure of the nicotinic acetylcholine receptor at 4Å resolution. J. Mol. Biol. 346 (2005) 967-989
27. VanLoock M.S., Yu X., et al. Complexes of RecA with LexA and RecX differentiate between active and inactive RecA nucleoprotein filaments. J. Mol. Biol. 333 (2003) 345-354
28. Wang H.W., and Nogales E. An iterative Fourier-Bessel algorithm for reconstruction of helical structures with severe Bessel overlap. J. Struct. Biol. 149 (2005) 65-78
29. 2+-ATPase. J. Mol. Biol. 316 (2002) 201-211
30. Yonekura K., Maki-Yonekura S., et al. Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Nature 424 (2003) 643-650
31. Yonekura K., and Toyoshima C. Structure determination of tubular crystals of membrane proteins. III. Solvent flattening. Ultramicroscopy 84 (2000) 29-45
32. Zhang P., Toyoshima C., et al. Structure of the calcium pump from sarcoplasmic reticulum at 8 Å resolution. Nature 392 (1998) 835-839