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Volumn 199, Issue 3, 2017, Pages 187-195

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

Author keywords

Contrast transfer function; Cryo electron microscopy; Defocus; Reconstruction; Subtomogram averaging; Tomography; Weighted back projection

Indexed keywords

ARTICLE; ELECTRON TOMOGRAPHY; IMAGE ANALYSIS; NOVA CONTRAST TRANSFER FUNCTION; PHYSICAL PARAMETERS; PRIORITY JOURNAL; SIMULATION; SOFTWARE; THREE DIMENSIONAL CONTRAST TRANSFER FUNCTION; THREE DIMENSIONAL IMAGING; VALIDATION PROCESS; WORKFLOW; CHEMISTRY; CRYOELECTRON MICROSCOPY; HUMAN IMMUNODEFICIENCY VIRUS 1; IMAGE PROCESSING; PROCEDURES; REPRODUCIBILITY;

EID: 85026294137     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2017.07.007     Document Type: Article
Times cited : (185)

References (30)
  • 1
    • 0021344602 scopus 로고
    • Simultaneous algebraic reconstruction technique (SART): a superior implementation of the ART algorithm
    • Andersen, A.H., Kak, A.C., Simultaneous algebraic reconstruction technique (SART): a superior implementation of the ART algorithm. Ultrason. Imag. 6 (1984), 81–94.
    • (1984) Ultrason. Imag. , vol.6 , pp. 81-94
    • Andersen, A.H.1    Kak, A.C.2
  • 2
    • 84947019114 scopus 로고    scopus 로고
    • Advances in single-particle electron cryomicroscopy structure determination applied to sub-tomogram averaging
    • 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 23 (2015), 1743–1753.
    • (2015) Structure , vol.23 , pp. 1743-1753
    • Bharat, T.A.M.1    Russo, C.J.2    Löwe, J.3    Passmore, L.A.4    Scheres, S.H.W.5
  • 3
    • 0000484921 scopus 로고
    • Inversion of fan-beam scans in radio astronomy
    • Bracewell, R.N., Riddle, A.C., Inversion of fan-beam scans in radio astronomy. Astrophys. J. 150 (1967), 427–434.
    • (1967) Astrophys. J. , vol.150 , pp. 427-434
    • Bracewell, R.N.1    Riddle, A.C.2
  • 4
    • 84878527131 scopus 로고    scopus 로고
    • Structural biology in situ – the potential of subtomogram averaging
    • Briggs, J.A., Structural biology in situ – the potential of subtomogram averaging. Curr. Opin. Struct. Biol. 23 (2013), 261–267.
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 261-267
    • Briggs, J.A.1
  • 5
    • 84894450833 scopus 로고    scopus 로고
    • Iterative reconstruction of cryo-electron tomograms using nonuniform fast fourier transforms
    • Chen, Y., Förster, F., Iterative reconstruction of cryo-electron tomograms using nonuniform fast fourier transforms. J. Struct. Biol. 185 (2013), 309–316.
    • (2013) J. Struct. Biol. , vol.185 , pp. 309-316
    • Chen, Y.1    Förster, F.2
  • 6
    • 84880607763 scopus 로고    scopus 로고
    • High-resolution noise substitution to measure overfitting and validate resolution in 3 d structure determination by single particle electron cryomicroscopy
    • 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 135 (2013), 24–35.
    • (2013) Ultramicroscopy , vol.135 , pp. 24-35
    • Chen, S.1    McMullan, G.2    Faruqi, A.R.3    Murshudov, G.N.4    Short, J.M.5    Scheres, S.H.W.6    Henderson, R.7
  • 7
    • 0014894609 scopus 로고
    • The reconstruction of a three-dimensional structure from projections and its application to electron microscopy
    • 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. 317 (1970), 319–340.
    • (1970) Proc. R. Soc. Lond. A. Math. Phys. Sci. , vol.317 , pp. 319-340
    • Crowther, R.A.1    DeRosier, D.J.2    Klug, A.3
  • 8
    • 48149106514 scopus 로고    scopus 로고
    • Restoration of weak phase-contrast images recorded with a high degree of defocus: the twin image problem associated with CTF correction
    • 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 108 (2008), 921–928.
    • (2008) Ultramicroscopy , vol.108 , pp. 921-928
    • Downing, K.H.1    Glaeser, R.M.2
  • 9
    • 33646784015 scopus 로고    scopus 로고
    • CTF determination and correction in electron cryotomography
    • Fernández, J.J., Li, S., Crowther, R.A., CTF determination and correction in electron cryotomography. Ultramicroscopy 106 (2006), 587–596.
    • (2006) Ultramicroscopy , vol.106 , pp. 587-596
    • Fernández, J.J.1    Li, S.2    Crowther, R.A.3
  • 10
    • 33847232164 scopus 로고    scopus 로고
    • Structure determination in situ by averaging of tomograms
    • J.R. McIntosh Academic Press
    • Förster, F., Hegerl, R., Structure determination in situ by averaging of tomograms. McIntosh, J.R., (eds.) Cellular electron microscopy Methods in Cell Biology, Vol. 79, 2007, Academic Press, 741–767.
    • (2007) Cellular electron microscopy, Methods in Cell Biology , vol.79 , pp. 741-767
    • Förster, F.1    Hegerl, R.2
  • 12
    • 0015523343 scopus 로고
    • The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. II. Direct methods
    • 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. 182 (July 1972), 89–102.
    • (1972) Proc. R. Soc. B Biol. Sci. , vol.182 , pp. 89-102
    • Gilbert, P.F.C.1
  • 13
    • 0039507411 scopus 로고
    • Structure of purple membrane from Halobacterium-halobium: recording, measurement and evaluation of electron micrographs at 3.5 A resolution
    • 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 19 (1986), 147–178.
    • (1986) Ultramicroscopy , vol.19 , pp. 147-178
    • Henderson, R.1    Baldwin, J.M.2    Downing, K.H.3    Lepault, J.4    Zemlin, F.5
  • 14
    • 0034039202 scopus 로고    scopus 로고
    • Defocus-gradient corrected backprojection
    • Jensen, G.J., Kornberg, R.D., Defocus-gradient corrected backprojection. Ultramicroscopy 84 (2000), 57–64.
    • (2000) Ultramicroscopy , vol.84 , pp. 57-64
    • Jensen, G.J.1    Kornberg, R.D.2
  • 15
    • 77955516433 scopus 로고    scopus 로고
    • Fully three-dimensional defocus-gradient corrected backprojection in cryoelectron microscopy
    • Kazantsev, I.G., Klukowska, J., Herman, G.T., Cernetic, L., Fully three-dimensional defocus-gradient corrected backprojection in cryoelectron microscopy. Ultramicroscopy 110 (2010), 1128–1142.
    • (2010) Ultramicroscopy , vol.110 , pp. 1128-1142
    • Kazantsev, I.G.1    Klukowska, J.2    Herman, G.T.3    Cernetic, L.4
  • 16
    • 0029879295 scopus 로고    scopus 로고
    • Computer visualization of three-dimensional image data using IMOD
    • Kremer, J.R., Mastronarde, D.N., McIntosh, J.R., Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116 (1996), 71–76.
    • (1996) J. Struct. Biol. , vol.116 , pp. 71-76
    • Kremer, J.R.1    Mastronarde, D.N.2    McIntosh, J.R.3
  • 17
    • 85003534346 scopus 로고    scopus 로고
    • Three-dimensional CTF correction improves the resolution of electron tomograms
    • Kunz, M., Frangakis, S.A., Three-dimensional CTF correction improves the resolution of electron tomograms. J. Struct. Biol. 197 (2017), 114–122.
    • (2017) J. Struct. Biol. , vol.197 , pp. 114-122
    • Kunz, M.1    Frangakis, S.A.2
  • 18
    • 0031422417 scopus 로고    scopus 로고
    • Dual-axis tomography: an approach with alignment methods that preserve resolution
    • Mastronarde, D.N., Dual-axis tomography: an approach with alignment methods that preserve resolution. J. Struct. Biol. 120 (1997), 343–352.
    • (1997) J. Struct. Biol. , vol.120 , pp. 343-352
    • Mastronarde, D.N.1
  • 20
    • 0038441501 scopus 로고    scopus 로고
    • Accurate determination of local defocus and specimen tilt in electron microscopy
    • Mindell, J.A., Grigorieff, N., Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142 (2003), 334–347.
    • (2003) J. Struct. Biol. , vol.142 , pp. 334-347
    • Mindell, J.A.1    Grigorieff, N.2
  • 21
    • 84946488108 scopus 로고    scopus 로고
    • CTFFIND4: fast and accurate defocus estimation from electron micrographs
    • Rohou, A., Grigorieff, N., CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192 (2015), 216–221.
    • (2015) J. Struct. Biol. , vol.192 , pp. 216-221
    • Rohou, A.1    Grigorieff, N.2
  • 22
    • 84888074636 scopus 로고    scopus 로고
    • Determination of protein structure at 8.5 resolution using cryo-electron tomography and sub-tomogram averaging
    • Schur, F.K.M., Hagen, W.J.H., de Marco, A., Briggs, J.A.G., Determination of protein structure at 8.5 resolution using cryo-electron tomography and sub-tomogram averaging. J. Struct. Biol. 184 (2013), 394–400.
    • (2013) J. Struct. Biol. , vol.184 , pp. 394-400
    • Schur, F.K.M.1    Hagen, W.J.H.2    de Marco, A.3    Briggs, J.A.G.4
  • 24
    • 84958979991 scopus 로고    scopus 로고
    • On geometric artifacts in cryo electron tomography
    • Turoňová, B., Marsalek, L., Slusallek, P., On geometric artifacts in cryo electron tomography. Ultramicroscopy 163 (2016), 48–61.
    • (2016) Ultramicroscopy , vol.163 , pp. 48-61
    • Turoňová, B.1    Marsalek, L.2    Slusallek, P.3
  • 26
    • 84994829249 scopus 로고    scopus 로고
    • Cryo-electron tomography and subtomogram averaging
    • Wan, W., Briggs, J.A.G., Cryo-electron tomography and subtomogram averaging. Methods Enzymol. 579 (2016), 329–367.
    • (2016) Methods Enzymol. , vol.579 , pp. 329-367
    • Wan, W.1    Briggs, J.A.G.2
  • 27
    • 0003574794 scopus 로고
    • Extrapolation, Interpolation, and Smoothing of Stationary Time Series, With Engineering Applications
    • Technology Press of the Massachusetts Institute of Technology Cambridge
    • Wiener, N., Extrapolation, Interpolation, and Smoothing of Stationary Time Series, With Engineering Applications. 1949, Technology Press of the Massachusetts Institute of Technology, Cambridge.
    • (1949)
    • Wiener, N.1
  • 29
    • 70349467745 scopus 로고    scopus 로고
    • Contrast transfer function correction applied to cryo-electron tomography and sub-tomogram averaging
    • Zanetti, G., Riches, J.D., Fuller, S.D., Briggs, J.A., Contrast transfer function correction applied to cryo-electron tomography and sub-tomogram averaging. J. Struct. Biol. 168 (2009), 305–312.
    • (2009) J. Struct. Biol. , vol.168 , pp. 305-312
    • Zanetti, G.1    Riches, J.D.2    Fuller, S.D.3    Briggs, J.A.4
  • 30
    • 84856199455 scopus 로고    scopus 로고
    • IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure
    • Zhang, L., Ren, G., IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure. PLoS One, 7, 2012, e30249.
    • (2012) PLoS One , vol.7 , pp. e30249
    • Zhang, L.1    Ren, G.2


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