메뉴 건너뛰기




Volumn 333, Issue 4, 2003, Pages 721-745

Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy

Author keywords

Absolute hand; Electron cryomicroscopy; Pyruvate dehydrogenase; Single particle reconstruction; Tilt pairs

Indexed keywords

DIHYDROLIPOAMIDE ACETYLTRANSFERASE; PYRUVATE DEHYDROGENASE;

EID: 0142042865     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.07.013     Document Type: Article
Times cited : (1713)

References (51)
  • 1
    • 0029003107 scopus 로고
    • The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules
    • Henderson R. The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules. Quart. Rev. Biophys. 28:1995;171-193.
    • (1995) Quart. Rev. Biophys. , vol.28 , pp. 171-193
    • Henderson, R.1
  • 2
    • 0023102907 scopus 로고
    • Angular reconstitution: A posteriori assignment of projection directions for 3D reconstruction
    • van Heel M. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy. 21:1987;111-124.
    • (1987) Ultramicroscopy , vol.21 , pp. 111-124
    • Van Heel, M.1
  • 3
    • 0031704540 scopus 로고    scopus 로고
    • A maximum-likelihood approach to single-particle image refinement
    • Sigworth F.J. A maximum-likelihood approach to single-particle image refinement. J. Struct. Biol. 122:1998;328-339.
    • (1998) J. Struct. Biol. , vol.122 , pp. 328-339
    • Sigworth, F.J.1
  • 4
    • 0013795002 scopus 로고
    • Structure of viruses of the papilloma-polyoma type III. Structure of rabbit papilloma virus with an appendix on the topography of contrast in negative-staining for electron-microscopy
    • Finch J.T., Klug A. Structure of viruses of the papilloma-polyoma type III. Structure of rabbit papilloma virus with an appendix on the topography of contrast in negative-staining for electron-microscopy. J. Mol. Biol. 13:1965;1-12.
    • (1965) J. Mol. Biol. , vol.13 , pp. 1-12
    • Finch, J.T.1    Klug, A.2
  • 5
    • 0013862410 scopus 로고
    • Arrangement of protein subunits and the distribution of nucleic acid in turnip yellow mosaic virus II. Electron microscopic studies
    • Finch J.T., Klug A. Arrangement of protein subunits and the distribution of nucleic acid in turnip yellow mosaic virus II. Electron microscopic studies. J. Mol. Biol. 15:1966;344-364.
    • (1966) J. Mol. Biol. , vol.15 , pp. 344-364
    • Finch, J.T.1    Klug, A.2
  • 6
    • 0015505844 scopus 로고
    • The hand of the helix of tobacco mosaic virus
    • Finch J.T. The hand of the helix of tobacco mosaic virus. J. Mol. Biol. 66:1972;291-294.
    • (1972) J. Mol. Biol. , vol.66 , pp. 291-294
    • Finch, J.T.1
  • 7
    • 0014413307 scopus 로고
    • Structure of viruses of the papilloma-polyoma type IV. Analysis of tilting experiments in the electron microscope
    • Klug A., Finch J.T. Structure of viruses of the papilloma-polyoma type IV. Analysis of tilting experiments in the electron microscope. J. Mol. Biol. 31:1968;1-12.
    • (1968) J. Mol. Biol. , vol.31 , pp. 1-12
    • Klug, A.1    Finch, J.T.2
  • 8
    • 0031257718 scopus 로고    scopus 로고
    • A method for establishing the handedness of biological macromolecules
    • Belnap D.M., Olson N.H., Baker T.S. A method for establishing the handedness of biological macromolecules. J. Struct. Biol. 120:1997;44-51.
    • (1997) J. Struct. Biol. , vol.120 , pp. 44-51
    • Belnap, D.M.1    Olson, N.H.2    Baker, T.S.3
  • 10
    • 0000984347 scopus 로고
    • Determination of absolute from relative X-ray intensity data
    • Wilson A.J.C. Determination of absolute from relative X-ray intensity data. Nature. 150:1942;152.
    • (1942) Nature , vol.150 , pp. 152
    • Wilson, A.J.C.1
  • 12
    • 3943108224 scopus 로고
    • Influence of electron noise on three-dimensional image reconstruction
    • Hegerl R., Hoppe W. Influence of electron noise on three-dimensional image reconstruction. Z. Naturforsch. 31a:1976;1717-1721.
    • (1976) Z. Naturforsch , vol.31 A , pp. 1717-1721
    • Hegerl, R.1    Hoppe, W.2
  • 14
    • 0026523919 scopus 로고
    • Image contrast in high-resolution electron microscopy of biological macromolecules: TMV in ice
    • Henderson R. Image contrast in high-resolution electron microscopy of biological macromolecules: TMV in ice. Ultramicroscopy. 46:1992;1-18.
    • (1992) Ultramicroscopy , vol.46 , pp. 1-18
    • Henderson, R.1
  • 15
    • 0028959025 scopus 로고
    • Three-dimensional structure of halorhodopsin at 7 Å resolution
    • Havelka W.A., Henderson R., Oesterhelt D. Three-dimensional structure of halorhodopsin at 7 Å resolution. J. Mol. Biol. 247:1995;726-738.
    • (1995) J. Mol. Biol. , vol.247 , pp. 726-738
    • Havelka, W.A.1    Henderson, R.2    Oesterhelt, D.3
  • 16
    • 0019987933 scopus 로고
    • The correlation averaging of a regularly arranged bacterial cell envelope protein
    • Saxton W.O., Baumeister W. The correlation averaging of a regularly arranged bacterial cell envelope protein. J. Microsc. 127:1982;127-138.
    • (1982) J. Microsc. , vol.127 , pp. 127-138
    • Saxton, W.O.1    Baumeister, W.2
  • 17
    • 0022128222 scopus 로고
    • Characteristic views of E. coli and B. stearothermophilus 30 S ribosomal subunits in the electron microscope
    • van Heel M., Stoffler-Meilicke M. Characteristic views of E. coli and B. stearothermophilus 30 S ribosomal subunits in the electron microscope. EMBO J. 4:1985;2389-2395.
    • (1985) EMBO J. , vol.4 , pp. 2389-2395
    • Van Heel, M.1    Stoffler-Meilicke, M.2
  • 18
    • 0001510472 scopus 로고
    • The treatment of errors in the isomorphous replacement method
    • Blow D.M., Crick F.H.C. The treatment of errors in the isomorphous replacement method. Acta Crystallog. 12:1959;794-802.
    • (1959) Acta Crystallog. , vol.12 , pp. 794-802
    • Blow, D.M.1    Crick, F.H.C.2
  • 19
    • 0033790516 scopus 로고    scopus 로고
    • Swinging arms and swinging domains in multifunctional enzymes: Catalytic machines for multistep reactions
    • Perham R.N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu. Rev. Biochem. 69:2000;961-1004.
    • (2000) Annu. Rev. Biochem. , vol.69 , pp. 961-1004
    • Perham, R.N.1
  • 20
    • 0033573917 scopus 로고    scopus 로고
    • Principles of quasi-equivalence and Euclidean geometry govern the assembly of cubic and dodecahedral cores of pyruvate dehydrogenase complexes
    • Izard T., Aevarsson A., Allen M.D., Westphal A.H., Perham R.N., de Kok A., Hol W.G. Principles of quasi-equivalence and Euclidean geometry govern the assembly of cubic and dodecahedral cores of pyruvate dehydrogenase complexes. Proc. Natl Acad. Sci. USA. 96:1999;1240-1245.
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 1240-1245
    • Izard, T.1    Aevarsson, A.2    Allen, M.D.3    Westphal, A.H.4    Perham, R.N.5    De Kok, A.6    Hol, W.G.7
  • 21
    • 18744386656 scopus 로고    scopus 로고
    • Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: A multifunctional catalytic machine
    • Milne J.L., Shi D., Rosenthal P.B., Sunshine J.S., Domingo G.J., Wu X., et al. Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine. EMBO J. 21:2002;5587-5598.
    • (2002) EMBO J. , vol.21 , pp. 5587-5598
    • Milne, J.L.1    Shi, D.2    Rosenthal, P.B.3    Sunshine, J.S.4    Domingo, G.J.5    Wu, X.6
  • 22
    • 0032053733 scopus 로고    scopus 로고
    • Evaluation of charging on macromolecules in electron cryomicroscopy
    • Brink J., Sherman M.B., Berriman J., Chiu W. Evaluation of charging on macromolecules in electron cryomicroscopy. Ultramicroscopy. 72:1998;41-52.
    • (1998) Ultramicroscopy , vol.72 , pp. 41-52
    • Brink, J.1    Sherman, M.B.2    Berriman, J.3    Chiu, W.4
  • 23
    • 0032540273 scopus 로고    scopus 로고
    • Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 Å in ice
    • Grigorieff N. Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 Å in ice. J. Mol. Biol. 277:1998;1033-1046.
    • (1998) J. Mol. Biol. , vol.277 , pp. 1033-1046
    • Grigorieff, N.1
  • 25
  • 26
    • 0027157439 scopus 로고
    • Refined crystal structure of the catalytic domain of dihydrolipoyl transacetylase (E2p) from Azotobacter vinelandii at 2.6 Å resolution
    • Mattevi A., Obmolova G., Kalk K.H., Westphal A.H., de Kok A., Hol W.G. Refined crystal structure of the catalytic domain of dihydrolipoyl transacetylase (E2p) from Azotobacter vinelandii at 2.6 Å resolution. J. Mol. Biol. 230:1993;1183-1199.
    • (1993) J. Mol. Biol. , vol.230 , pp. 1183-1199
    • Mattevi, A.1    Obmolova, G.2    Kalk, K.H.3    Westphal, A.H.4    De Kok, A.5    Hol, W.G.6
  • 27
    • 0035783389 scopus 로고    scopus 로고
    • Alignment error envelopes for single particle analysis
    • Jensen G.J. Alignment error envelopes for single particle analysis. J. Struct. Biol. 133:2001;143-155.
    • (2001) J. Struct. Biol. , vol.133 , pp. 143-155
    • Jensen, G.J.1
  • 28
    • 0033066115 scopus 로고    scopus 로고
    • Solution X-ray scattering-based estimation of electron cryomicroscopy imaging parameters for reconstruction of virus particles
    • Thuman-Commike P.A., Tsuruta H., Greene B., Prevelige P.E. Jr, King J., Chiu W. Solution X-ray scattering-based estimation of electron cryomicroscopy imaging parameters for reconstruction of virus particles. Biophys. J. 76:1999;2249-2261.
    • (1999) Biophys. J. , vol.76 , pp. 2249-2261
    • Thuman-Commike, P.A.1    Tsuruta, H.2    Greene, B.3    Prevelige P.E., Jr.4    King, J.5    Chiu, W.6
  • 29
    • 0035782663 scopus 로고    scopus 로고
    • Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination
    • Saad A., Ludtke S.J., Jakana J., Rixon F.J., Tsuruta H., Chiu W. Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination. J. Struct. Biol. 133:2001;32-42.
    • (2001) J. Struct. Biol. , vol.133 , pp. 32-42
    • Saad, A.1    Ludtke, S.J.2    Jakana, J.3    Rixon, F.J.4    Tsuruta, H.5    Chiu, W.6
  • 30
    • 0033377941 scopus 로고    scopus 로고
    • Review: Electron crystallography: Present excitement, a nod to the past, anticipating the future
    • Glaeser R.M. Review: electron crystallography: present excitement, a nod to the past, anticipating the future. J. Struct. Biol. 128:1999;3-14.
    • (1999) J. Struct. Biol. , vol.128 , pp. 3-14
    • Glaeser, R.M.1
  • 32
    • 1842409555 scopus 로고    scopus 로고
    • Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy
    • Böttcher B., Wynne S.A., Crowther R.A. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature. 386:1997;88-91.
    • (1997) Nature , vol.386 , pp. 88-91
    • Böttcher, B.1    Wynne, S.A.2    Crowther, R.A.3
  • 34
    • 0035877764 scopus 로고    scopus 로고
    • Direct evidence for the size and conformational variability of the pyruvate dehydrogenase complex revealed by three-dimensional electron microscopy. The "breathing" core and its functional relationship to protein dynamics
    • Zhou Z.H., Liao W., Cheng R.H., Lawson J.E., McCarthy D.B., Reed L.J., Stoops J.K. Direct evidence for the size and conformational variability of the pyruvate dehydrogenase complex revealed by three-dimensional electron microscopy. The "breathing" core and its functional relationship to protein dynamics. J. Biol. Chem. 276:2001;21704-21713.
    • (2001) J. Biol. Chem. , vol.276 , pp. 21704-21713
    • Zhou, Z.H.1    Liao, W.2    Cheng, R.H.3    Lawson, J.E.4    McCarthy, D.B.5    Reed, L.J.6    Stoops, J.K.7
  • 35
    • 0030758675 scopus 로고    scopus 로고
    • The catalytic domain of dihydrolipoyl acetyltransferase from the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus. Expression, purification and reversible denaturation
    • Allen M.D., Perham R.N. The catalytic domain of dihydrolipoyl acetyltransferase from the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus. Expression, purification and reversible denaturation. FEBS Letters. 413:1997;339-343.
    • (1997) FEBS Letters , vol.413 , pp. 339-343
    • Allen, M.D.1    Perham, R.N.2
  • 36
    • 0037751777 scopus 로고
    • Holey films for electron microscopy
    • Harris J.W. Holey films for electron microscopy. Nature. 196:1962;499-500.
    • (1962) Nature , vol.196 , pp. 499-500
    • Harris, J.W.1
  • 37
    • 0023889015 scopus 로고
    • Containment system for the preparation of vitrified-hydrated virus specimens
    • Jeng T.W., Talmon Y., Chiu W. Containment system for the preparation of vitrified-hydrated virus specimens. J. Electron Microsc. Tech. 8:1988;343-348.
    • (1988) J. Electron Microsc. Tech. , vol.8 , pp. 343-348
    • Jeng, T.W.1    Talmon, Y.2    Chiu, W.3
  • 39
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A. 47:1991;110-119.
    • (1991) Acta Crystallog. sect. A , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 40
    • 0029185933 scopus 로고
    • CRYSOL - A program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates
    • Svergun D., Barberato C., Koch M.H.J. CRYSOL - a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallog. 28:1995;768-773.
    • (1995) J. Appl. Crystallog. , vol.28 , pp. 768-773
    • Svergun, D.1    Barberato, C.2    Koch, M.H.J.3
  • 41
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D. 50:1994;760-763.
    • (1994) Acta Crystallog. sect. D , vol.50 , pp. 760-763
  • 44
    • 0019987933 scopus 로고
    • The correlation averaging of a regularly arranged bacterial cell envelope protein
    • Saxton W.O., Baumeister W. The correlation averaging of a regularly arranged bacterial cell envelope protein. J. Microsc. 127:1982;127-138.
    • (1982) J. Microsc. , vol.127 , pp. 127-138
    • Saxton, W.O.1    Baumeister, W.2
  • 45
    • 0022128222 scopus 로고
    • Characteristic views of E. coli and B. stearothermophilus 30 S ribosomal subunits in the electron microscope
    • van Heel M., Stoffler-Meilicke M. Characteristic views of E. coli and B. stearothermophilus 30 S ribosomal subunits in the electron microscope. EMBO J. 4:1985;2389-2395.
    • (1985) EMBO J. , vol.4 , pp. 2389-2395
    • Van Heel, M.1    Stoffler-Meilicke, M.2
  • 46
    • 0023090371 scopus 로고
    • Similarity measures between images
    • van Heel M. Similarity measures between images. Ultramicroscopy. 21:1987;95-100.
    • (1987) Ultramicroscopy , vol.21 , pp. 95-100
    • Van Heel, M.1
  • 47
    • 0031583477 scopus 로고    scopus 로고
    • Structure of keyhole limpet hemocyanin type 1 (KLH1) at 15 Å resolution by electron cryomicroscopy and angular reconstitution
    • Orlova E.V., Dube P., Harris J.R., Beckman E., Zemlin F., Markl J., van Heel M., et al. Structure of keyhole limpet hemocyanin type 1 (KLH1) at 15 Å resolution by electron cryomicroscopy and angular reconstitution. J. Mol. Biol. 271:1997;417-437.
    • (1997) J. Mol. Biol. , vol.271 , pp. 417-437
    • Orlova, E.V.1    Dube, P.2    Harris, J.R.3    Beckman, E.4    Zemlin, F.5    Markl, J.6    Van Heel, M.7
  • 48
    • 0000167776 scopus 로고    scopus 로고
    • Appendix: Measures of resolution using Fourier shell correlation
    • Penczek P. Appendix: measures of resolution using Fourier shell correlation. J. Mol. Biol. 280:1998;115-116.
    • (1998) J. Mol. Biol. , vol.280 , pp. 115-116
    • Penczek, P.1
  • 49
    • 0033777020 scopus 로고    scopus 로고
    • Resolution measurement in structures derived from single particles
    • Grigorieff N. Resolution measurement in structures derived from single particles. Acta Crystallog. sect. D. 56:2000;1270-1277.
    • (2000) Acta Crystallog. sect. D , vol.56 , pp. 1270-1277
    • Grigorieff, N.1
  • 50
    • 0001510472 scopus 로고
    • The treatment of errors in the isomorphous replacement method
    • Blow D.M., Crick F.H.C. The treatment of errors in the isomorphous replacement method. Acta Crystallog. 12:1959;794-802.
    • (1959) Acta Crystallog. , vol.12 , pp. 794-802
    • Blow, D.M.1    Crick, F.H.C.2
  • 51
    • 0000552208 scopus 로고
    • Phase error and the map correlation coefficient
    • Lunin V.Y., Woolfson M.M. Phase error and the map correlation coefficient. Acta Crystallog. sect. D. 49:1993;530-533.
    • (1993) Acta Crystallog. sect. D , vol.49 , pp. 530-533
    • Lunin, V.Y.1    Woolfson, M.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.