Conical fourier shell correlation applied to electron tomograms

Journal of Structural Biology

Volumn 190, Issue 2, 2015, Pages 215-223

  Diebolder, C A ^a,b   Faas, F G A ^a   Koster, A J ^a   Koning, R I ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b UTRECHT UNIVERSITY   (Netherlands)

Author keywords

Conical fourier shell correlation; Cryo electron microscopy; Dual axis cryo electron tomography; Fourier shell correlation; Resolution estimation

Indexed keywords

ARTICLE; CONTROLLED STUDY; ELECTRON BEAM; ELECTRON RADIATION; ELECTRON TOMOGRAPHY; IMAGE RECONSTRUCTION; NONHUMAN; PRIORITY JOURNAL; SIMULATION; ANISOTROPY; COMPARATIVE STUDY; COMPUTER SIMULATION; CRYOELECTRON MICROSCOPY; FOURIER ANALYSIS; IMAGE PROCESSING; PROCEDURES; RADIATION RESPONSE;

ANISOTROPY; COMPUTER SIMULATION; CRYOELECTRON MICROSCOPY; DOSE-RESPONSE RELATIONSHIP, RADIATION; ELECTRON MICROSCOPE TOMOGRAPHY; FOURIER ANALYSIS; IMAGE PROCESSING, COMPUTER-ASSISTED;

EID: 84928694869     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2015.03.010     Document Type: Article

References (40)

1. Amunts A., Brown A., Bai X.c., Llacer J.L., Hussain T., Emsley P., Long F., Murshudov G., Scheres S.H., Ramakrishnan V. Structure of the yeast mitochondrial large ribosomal subunit. Science 2014, 343:1485-1489.
2. Boettcher B., Wynne S.A., Crowther R.A. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature 1997, 386:88-91.
3. Bracewell R.N., Riddle A.C. Inversion of fan-beam scans in radio astronomy. Astrophys J 1967, 150:427.
4. Cantele F., Paccagnini E., Pigino G., Lupetti P., Lanzavecchia S. Simultaneous alignment of dual-axis tilt series. J. Struct. Biol. 2010, 169:192-199.
5. Cardone G., Grünewald K., Steven A.C. A resolution criterion for electron tomography based on cross-validation. J. Struct. Biol. 2005, 151:117-129.
6. Chen D., Friedrich H., With G.d. On resolution in electron tomography of beam sensitive materials. J. Phys. Chem. C 2014, 118:1248-1257.
7. Claassen I., Meylis J., van der Ley P., Peeters C., Brons H., Robert J., Borsboom D., van der Ark A., van Straaten I., Roholl P. Production, characterization and control of a Neisseria meningitidis hexavalent class 1 outer membrane protein containing vesicle vaccine. Vaccine 1996, 14:1001-1008.
8. Diebolder C.A., Koster A.J., Koning R.I. Pushing the resolution limits in cryo electron tomography of biological structures. J. Microsc. 2012, 248:1-5.
9. Diebolder C.A., Beurskens F.J., de Jong R.N., Koning R.I., Strumane K., Lindorfer M.A., Voorhorst M., Ugurlar D., Rosati S., Heck A.J., van de Winkel J.G., Wilson I.A., Koster A.J., Taylor R.P., Ollmann Saphire E., Burton D.R., Schuurman J., Gros P., Parren P.W. Complement is activated by IgG hexamers assembled at the cell surface. Science 2014, 343:1260-1263.
10. Dudkina N.V., Oostergetel G.T., Lewejohann D., Braun H.P., Boekema E.J. Row-like organization of ATP synthase in intact mitochondria determined by cryo-electron tomography. Biochim. Biophys. Acta (BBA)-Bioenerg. 2010, 1797:272-277.
11. Fernandez J.J., Li S., Crowther R.A. CTF determination and correction in electron cryotomography. Ultramicroscopy 2006, 106:587-596.
12. Frangakis A.S., Hegerl R. Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion. J. Struct. Biol. 2001, 135:239-250.
13. Frank J., Al-Ali L. Signal-to-noise ratio of electron micrographs obtained by cross correlation. Nature 1975, 256:376-379.
14. Guesdon A., Blestel S., Kervrann C., Crétien D. Single versus dual-axis cryo-electron tomography of microtubules assembled in vitro: limits and perspectives. J. Struct. Biol. 2013, 181:169-178.
15. Harauz G., van Heel M. Exact filters for general geometry three dimensional reconstruction. Proc. IEEE Comput. Vision Pattern Recognit. Conf. 1986, 73:146-156.
16. Heidari Mezerji H., Van den Broek W., Bals S. A practical method to determine the effective resolution in incoherent experimental electron tomography. Ultramicroscopy 2011, 111:330-336.
17. Hendriks, C.L., Van Vliet, L.J., Rieger, B., van Kempen, G.M.P., van Ginkel, M. 1999. DIPimage: A Scientific Image Processing Toolbox for MATLAB. Quantitative Imaging Group, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands.
18. Heymann J.B., Belnap D.M. Bsoft: image processing and molecular modeling for electron microscopy. J. Struct. Biol. 2007, 157:3-18.
19. Iancu C.V., Wright E.R., Benjamin J., Tivol W.F., Dias D.P., Murphy G.E., Morrison R.C., Heymann J.B., Jensen G.J. A "flip-flop" rotation stage for routine dual-axis electron cryotomography. J. Struct. Biol. 2005, 151:288-297.
20. Kremer J.R., Mastronarde D.N., McIntosh J.R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 1996, 116:71-76.
21. Lanzavecchia S., Cantele F., Bellon P.L., Zampighi L., Kreman M., Wright E., Zampighi G.A. Conical tomography of freeze-fracture replicas: a method for the study of integral membrane proteins inserted in phospholipid bilayers. J. Struct. Biol. 2005, 149:87-98.
22. Met and fitting of L1 protein. J. Mol. Biol. 1998, 280:103-116.
23. Mastronarde D.N. Dual-axis tomography: an approach with alignment methods that preserve resolution. J. Struct. Biol. 1997, 120:343-352.
24. Myasnikov A.G., Afonina Z.A., Klaholz B.P. Single particle and molecular assembly analysis of polyribosomes by single-and double-tilt cryo electron tomography. Ultramicroscopy 2013, 126:33-39.
25. Nickell S., Hegerl R., Baumeister W., Rachel R. Pyrodictium cannulae enter the periplasmic space but do not enter the cytoplasm, as revealed by cryo-electron tomography. J. Struct. Biol. 2003, 141:34-42.
26. Penczek P.A., Frank J. Resolution in electron tomography. Electron Tomogr. 2006, 307-330.
27. Penczek P.A., Marko M., Buttle K., Frank J. Double-tilt electron tomography. Ultramicroscopy 1995, 60:393-410.
28. Penczek P.A. Three-dimensional spectral signal-to-noise ratio for a class of reconstruction algorithms. J. Struct. Biol. 2002, 138:34-46.
29. Penczek P.A. Resolution measures in molecular electron microscopy. Methods Enzymol. 2010, 482:73-100.
30. Rosenthal P.B., Henderson R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 2003, 333:721-745.
31. Saff E.B., Kuijlaars A.B. Distributing many points on a sphere. Math. Intell. 1997, 19:5-11.
32. Saxton W.O., Baumeister W. The correlation averaging of a regularly arranged bacterial cell envelope protein. J. Microsc. 1982, 127:127-138.
33. Schoenmakers R.H.M., Perquin R.A., Fliervoet T.F., Voorhout W., Schirmacher H. New software for high resolution, high throughput electron tomography. Microsc. Anal. 2005, 19:5-6.
34. Unser M., Sorzano C.S., Thevenaz P., Jonic S., El-Bez C., De Carlo S., Conway J.F., Trus B.L. Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions. J. Struct. Biol. 2005, 149:243-255.
35. van Heel M. Detection of objects in quantum-noise-limited images. Ultramicroscopy 1982, 7:331-341.
36. van Heel M., Harauz G. Resolution criteria for three dimensional reconstruction. Optik 1986, 73:119-122.
37. van Heel M., Schatz M. Fourier shell correlation threshold criteria. J. Struct. Biol. 2005, 151:250-262.
38. Winkler H., Taylor K.A. Marker-free dual-axis tilt series alignment. J. Struct. Biol. 2013, 182:117-124.
39. Wu S., Liu J., Reedy M.C., Winkler H., Reedy M.K., Taylor K.A. Methods for identifying and averaging variable molecular conformations in tomograms of actively contracting insect flight muscle. J. Struct. Biol. 2009, 168:485-502.
40. Zhang X., Jin L., Fang Q., Hui W.H., Zhou Z.H. 3.3 A cryo-EM structure of a nonenveloped virus reveals a priming mechanism for cell entry. Cell 2010, 141:472-482.