publication . Article . Other literature type . 2017

Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å.

Beata Turoňová; Florian K.M. Schur; William Wan; John A.G. Briggs;
Open Access English
  • Published: 01 Sep 2017 Journal: Journal of Structural Biology, volume 199, issue 3, pages 187-195 (issn: 1047-8477, eissn: 1095-8657, Copyright policy)
  • Publisher: Academic Press
Abstract
Abstract Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular complexes to be imaged in three-dimensions in their native environments. Cryo-electron tomograms are reconstructed from projection images taken at defined tilt-angles. In order to recover high-resolution information from cryo-electron tomograms, it is necessary to measure and correct for the contrast transfer function (CTF) of the microscope. Most commonly, this is performed using protocols that approximate the sample as a two-dimensional (2D) plane. This approximation accounts for differences in defocus and therefore CTF across the tilted sample. It does not account f...
Subjects
free text keywords: Article, Cryo-electron microscopy, Tomography, Contrast transfer function, Subtomogram averaging, Defocus, Reconstruction, Weighted back projection, Structural Biology, Cryo-electron tomography, Synthetic data, Microscope, law.invention, law, Macromolecular Complexes, Crystallography, Biology
Funded by
EC| MEMBRANEFUSION
Project
MEMBRANEFUSION
Structure and mechanism of viral and cellular membrane fusion machineries
  • Funder: European Commission (EC)
  • Project Code: 648432
  • Funding stream: H2020 | ERC | ERC-COG
30 references, page 1 of 2

Andersen, A.H., Kak, A.C.. Simultaneous algebraic reconstruction technique (SART): a superior implementation of the ART algorithm. Ultrason. Imag.. 1984; 6: 81-94

Bharat, T.A.M., Russo, C.J., Löwe, J., Passmore, L.A., Scheres, S.H.W.. Advances in single-particle electron cryomicroscopy structure determination applied to sub-tomogram averaging. Structure. 2015; 23: 1743-1753 [OpenAIRE] [PubMed]

Bracewell, R.N., Riddle, A.C.. Inversion of fan-beam scans in radio astronomy. Astrophys. J.. 1967; 150: 427-434 [OpenAIRE]

Briggs, J.A.. Structural biology in situ – the potential of subtomogram averaging. Curr. Opin. Struct. Biol.. 2013; 23: 261-267 [PubMed]

Chen, Y., Förster, F.. Iterative reconstruction of cryo-electron tomograms using nonuniform fast fourier transforms. J. Struct. Biol.. 2013; 185: 309-316 [PubMed]

Chen, S., McMullan, G., Faruqi, A.R., Murshudov, G.N., Short, J.M., Scheres, S.H.W., Henderson, R.. High-resolution noise substitution to measure overfitting and validate resolution in 3 d structure determination by single particle electron cryomicroscopy. Ultramicroscopy. 2013; 135: 24-35 [OpenAIRE] [PubMed]

Crowther, R.A., DeRosier, D.J., Klug, A.. The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. Proc. R. Soc. Lond. A. Math. Phys. Sci.. 1970; 317: 319-340

Downing, K.H., Glaeser, R.M.. Restoration of weak phase-contrast images recorded with a high degree of defocus: the twin image problem associated with CTF correction. Ultramicroscopy. 2008; 108: 921-928 [OpenAIRE] [PubMed]

Fernández, J.J., Li, S., Crowther, R.A.. CTF determination and correction in electron cryotomography. Ultramicroscopy. 2006; 106: 587-596 [PubMed]

Förster, F., Hegerl, R., McIntosh, J.R.. Cellular electron microscopy. 2007; Vol. 79: 741-767

Förster, F., Han, B.G., Beck, M.. Visual proteomics. Methods Enzymol.. 2010; 483: 215-243 [PubMed]

Gilbert, P.F.C.. The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. II. Direct methods. Proc. R. Soc. B Biol. Sci.. July 1972; 182: 89-102 [PubMed]

Henderson, R., Baldwin, J.M., Downing, K.H., Lepault, J., Zemlin, F.. Structure of purple membrane from Halobacterium-halobium: recording, measurement and evaluation of electron micrographs at 3.5 A resolution. Ultramicroscopy. 1986; 19: 147-178

Jensen, G.J., Kornberg, R.D.. Defocus-gradient corrected backprojection. Ultramicroscopy. 2000; 84: 57-64 [PubMed]

Kazantsev, I.G., Klukowska, J., Herman, G.T., Cernetic, L.. Fully three-dimensional defocus-gradient corrected backprojection in cryoelectron microscopy. Ultramicroscopy. 2010; 110: 1128-1142 [OpenAIRE] [PubMed]

30 references, page 1 of 2
Abstract
Abstract Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular complexes to be imaged in three-dimensions in their native environments. Cryo-electron tomograms are reconstructed from projection images taken at defined tilt-angles. In order to recover high-resolution information from cryo-electron tomograms, it is necessary to measure and correct for the contrast transfer function (CTF) of the microscope. Most commonly, this is performed using protocols that approximate the sample as a two-dimensional (2D) plane. This approximation accounts for differences in defocus and therefore CTF across the tilted sample. It does not account f...
Subjects
free text keywords: Article, Cryo-electron microscopy, Tomography, Contrast transfer function, Subtomogram averaging, Defocus, Reconstruction, Weighted back projection, Structural Biology, Cryo-electron tomography, Synthetic data, Microscope, law.invention, law, Macromolecular Complexes, Crystallography, Biology
Funded by
EC| MEMBRANEFUSION
Project
MEMBRANEFUSION
Structure and mechanism of viral and cellular membrane fusion machineries
  • Funder: European Commission (EC)
  • Project Code: 648432
  • Funding stream: H2020 | ERC | ERC-COG
30 references, page 1 of 2

Andersen, A.H., Kak, A.C.. Simultaneous algebraic reconstruction technique (SART): a superior implementation of the ART algorithm. Ultrason. Imag.. 1984; 6: 81-94

Bharat, T.A.M., Russo, C.J., Löwe, J., Passmore, L.A., Scheres, S.H.W.. Advances in single-particle electron cryomicroscopy structure determination applied to sub-tomogram averaging. Structure. 2015; 23: 1743-1753 [OpenAIRE] [PubMed]

Bracewell, R.N., Riddle, A.C.. Inversion of fan-beam scans in radio astronomy. Astrophys. J.. 1967; 150: 427-434 [OpenAIRE]

Briggs, J.A.. Structural biology in situ – the potential of subtomogram averaging. Curr. Opin. Struct. Biol.. 2013; 23: 261-267 [PubMed]

Chen, Y., Förster, F.. Iterative reconstruction of cryo-electron tomograms using nonuniform fast fourier transforms. J. Struct. Biol.. 2013; 185: 309-316 [PubMed]

Chen, S., McMullan, G., Faruqi, A.R., Murshudov, G.N., Short, J.M., Scheres, S.H.W., Henderson, R.. High-resolution noise substitution to measure overfitting and validate resolution in 3 d structure determination by single particle electron cryomicroscopy. Ultramicroscopy. 2013; 135: 24-35 [OpenAIRE] [PubMed]

Crowther, R.A., DeRosier, D.J., Klug, A.. The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. Proc. R. Soc. Lond. A. Math. Phys. Sci.. 1970; 317: 319-340

Downing, K.H., Glaeser, R.M.. Restoration of weak phase-contrast images recorded with a high degree of defocus: the twin image problem associated with CTF correction. Ultramicroscopy. 2008; 108: 921-928 [OpenAIRE] [PubMed]

Fernández, J.J., Li, S., Crowther, R.A.. CTF determination and correction in electron cryotomography. Ultramicroscopy. 2006; 106: 587-596 [PubMed]

Förster, F., Hegerl, R., McIntosh, J.R.. Cellular electron microscopy. 2007; Vol. 79: 741-767

Förster, F., Han, B.G., Beck, M.. Visual proteomics. Methods Enzymol.. 2010; 483: 215-243 [PubMed]

Gilbert, P.F.C.. The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. II. Direct methods. Proc. R. Soc. B Biol. Sci.. July 1972; 182: 89-102 [PubMed]

Henderson, R., Baldwin, J.M., Downing, K.H., Lepault, J., Zemlin, F.. Structure of purple membrane from Halobacterium-halobium: recording, measurement and evaluation of electron micrographs at 3.5 A resolution. Ultramicroscopy. 1986; 19: 147-178

Jensen, G.J., Kornberg, R.D.. Defocus-gradient corrected backprojection. Ultramicroscopy. 2000; 84: 57-64 [PubMed]

Kazantsev, I.G., Klukowska, J., Herman, G.T., Cernetic, L.. Fully three-dimensional defocus-gradient corrected backprojection in cryoelectron microscopy. Ultramicroscopy. 2010; 110: 1128-1142 [OpenAIRE] [PubMed]

30 references, page 1 of 2
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publication . Article . Other literature type . 2017

Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å.

Beata Turoňová; Florian K.M. Schur; William Wan; John A.G. Briggs;