Structure Determination In Situ by Averaging of Tomograms

Methods in Cell Biology - Tập 79 - Trang 741-767 - 2007
Friedrich Förster1, Reiner Hegerl2
1Department of Pharmaceutical Sciences, University of California, San Francisco, California 94143
2Max‐Planck Institute of Biochemistry, Am Klopferspitz 18, D‐82152 Martinsried, Germany

Tài liệu tham khảo

Beck, 2004, Nuclear pore complex structure and dynamics revealed by cryoelectron tomography, Science, 306, 1387, 10.1126/science.1104808 Benjamin, 2005, Three‐dimensional structure of HIV‐1 virus‐like particles by electron cryotomography, J. Mol. Biol., 346, 577, 10.1016/j.jmb.2004.11.064 Briggs, 2006, The Mechanism of HIV‐1 core assembly: Insights from three‐dimensional reconstructions of authentic virions, Structure, 14, 15, 10.1016/j.str.2005.09.010 Carazo, 1992, The fidelity of 3D reconstructions from incomplete data and the use of restoration methods Chen, 1996, IVE (Image Visualization Environment): A software platform for all three‐dimensional microscopy applications, J. Struct. Biol., 116, 56, 10.1006/jsbi.1996.0010 Crowther, 1970, The reconstruction of a three‐dimensional structure from its projections and its applications to electron microscopy, Proc. R. Soc. Lond., 317, 319, 10.1098/rspa.1970.0119 Cyrklaff, 2005, Cryo‐electron tomography of vaccinia virus, Proc. Natl. Acad. Sci. USA, 102, 2772, 10.1073/pnas.0409825102 DeRosier, 1968, Reconstruction of three‐dimensional structures from electron micrographs, Nature, 217, 130, 10.1038/217130a0 Diez, 2006, Tilt‐series and electron microscope alignment for the correction of the non‐perpendicularity of beam and tilt‐axis, J. Struct. Biol., 154, 195, 10.1016/j.jsb.2005.12.009 Dubochet, 1988, Cryo‐electron microscopy of vitrified specimens, Q. Rev. Biophys., 21, 129, 10.1017/S0033583500004297 Förster, 2005, Retrovirus envelope protein complex structure in situ determined by cryo‐electron tomography, Proc. Natl. Acad. Sci. USA, 102, 4729, 10.1073/pnas.0409178102 Frangakis, 2002, Identification of macromolecular complexes in cryoelectron tomograms of phantom cells, Proc. Natl. Acad. Sci. USA, 99, 14153, 10.1073/pnas.172520299 Frangakis, 2004, Computational exploration of structural information from cryo‐electron tomograms, Curr. Opin. Struct. Biol., 14, 325, 10.1016/j.sbi.2004.04.003 Frank, 1996 Frank, 2002, Single‐particle imaging of macromolecules by cryo‐electron microscopy, Annu. Rev. Biophys. Biomol. Struct., 31, 303, 10.1146/annurev.biophys.31.082901.134202 Gonen, 2005, Lipid–protein interactions in double‐layered two‐dimensional AQP0 crystals, Nature, 438, 633, 10.1038/nature04321 Grigorieff, 2000, Resolution measurement in structures derived from single particles, Acta Crystallogr. D Biol. Crystallogr., 56, 1270, 10.1107/S0907444900009549 Grimm, 1996, Zero‐loss energy‐filtering under low‐dose conditions using a postcolumn energy filter, J. Microsc., 183, 60, 10.1046/j.1365-2818.1996.77441.x Grünewald, 2003, Three‐dimensional structure of herpes simplex virus from cryo‐electron tomography, Science, 302, 1396, 10.1126/science.1090284 Harauz, 1986, Exact filter for general geometry three‐dimensional reconstruction, Optik, 73, 146 Henderson, 2004, Realizing the potential of electron cryo‐microscopy, Q. Rev. Biophys., 37, 3, 10.1017/S0033583504003920 Hsieh, 2006, Towards high‐resolution three‐dimensional imaging of native mammalian tissue: Electron tomography of frozen‐hydrated rat liver sections, J. Struct. Biol., 153, 1, 10.1016/j.jsb.2005.10.004 Hunziker, 1984, Cartilage ultrastructure after high pressure freezing, freeze substitution, and low temperature embedding. I. Chondrocyte ultrastructure–implications for the theories of mineralization and vascular invasion, J. Cell Biol., 98, 267, 10.1083/jcb.98.1.267 Iancu, 2005, A “flip‐flop” rotation stage for routine dual‐axis electron cryotomography, J. Struct. Biol., 151, 288, 10.1016/j.jsb.2005.07.004 Knauer, 1983, Three‐dimensional reconstruction and averaging of 30 S ribosomal subunits of Escherichia coli from electron micrographs, J. Mol. Biol., 163, 409, 10.1016/0022-2836(83)90066-9 Koster, 1997, Perspectives of molecular and cellular electron tomography, J. Struct. Biol., 120, 276, 10.1006/jsbi.1997.3933 Kremer, 1996, Computer visualization of three‐dimensional image data using IMOD, J. Struct. Biol., 116, 71, 10.1006/jsbi.1996.0013 Kurner, 2005, Cryo‐electron tomography reveals the cytoskeletal structure of Spiroplasma melliferum, Science, 307, 436, 10.1126/science.1104031 Ladinsky, 1999, Golgi structure in three dimensions: Functional insights from the normal rat kidney cell, J. Cell Biol., 144, 1135, 10.1083/jcb.144.6.1135 Lawrence, 2006, Transform‐based backprojection for volume reconstruction of large format electron microscope tilt series, J. Struct. Biol., 154, 144, 10.1016/j.jsb.2005.12.012 Lawrence, 1992, Least‐squares method of alignment using markers Lucic, 2005, Structural studies by electron tomography: From cells to molecules, Annu. Rev. Biochem., 74, 833, 10.1146/annurev.biochem.73.011303.074112 Ludtke, 1999, EMAN: Semiautomated software for high‐resolution single‐particle reconstructions, J. Struct. Biol., 128, 82, 10.1006/jsbi.1999.4174 Marsh, 2001, Organellar relationships in the Golgi region of the pancreatic beta cell line, HIT‐T15, visualized by high resolution electron tomography, Proc. Natl. Acad. Sci. USA, 98, 2399, 10.1073/pnas.051631998 Marsh, 2004, Direct continuities between cisternae at different levels of the Golgi complex in glucose‐stimulated mouse islet beta cells, Proc. Natl. Acad. Sci. USA, 101, 5565, 10.1073/pnas.0401242101 Mastronarde, 1997, Dual‐axis tomography: An approach with alignment methods that preserve resolution, J. Struct. Biol., 120, 343, 10.1006/jsbi.1997.3919 Mastronarde, 2005, Automated electron microscope tomography using robust prediction of specimen movements, J. Struct. Biol., 152, 36, 10.1016/j.jsb.2005.07.007 McDonald, 1993, Improved preservation of ultrastructure in difficult‐to‐fix organisms by high pressure freezing and freeze substitution: I. Drosophila melanogaster and Strongylocentrotus purpuratus embryos, Microsc. Res. Tech., 24, 465, 10.1002/jemt.1070240603 McIntosh, 2005, New views of cells in 3D: An introduction to electron tomography, Trends Cell Biol., 15, 43, 10.1016/j.tcb.2004.11.009 Medalia, 2002, Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography, Science, 298, 1209, 10.1126/science.1076184 Miyazawa, 2003, Structure and gating mechanism of the acetylcholine receptor pore, Nature, 423, 949, 10.1038/nature01748 Moritz, 2000, Structure of the gamma‐tubulin ring complex: A template for microtubule nucleation, Nat. Cell Biol., 2, 365, 10.1038/35014058 Murk, 2003, Endosomal compartmentalization in three dimensions: Implications for membrane fusion, Proc. Natl. Acad. Sci. USA, 100, 13332, 10.1073/pnas.2232379100 Murk, 2003, Influence of aldehyde fixation on the morphology of endosomes and lysosomes: Quantitative analysis and electron tomography, J. Microsc., 212, 81, 10.1046/j.1365-2818.2003.01238.x Navaza, 2003, On the three‐dimensional reconstruction of icosahedral particles, J. Struct. Biol., 144, 13, 10.1016/j.jsb.2003.09.007 Nicastro, 2000, Cryo‐electron tomography of neurospora mitochondria, J. Struct. Biol., 129, 48, 10.1006/jsbi.1999.4204 Nicastro, 2005, 3D structure of eukaryotic flagella in a quiescent state revealed by cryo‐electron tomography, Proc. Natl. Acad. Sci. USA, 102, 15889, 10.1073/pnas.0508274102 Nickell, 2005, TOM toolbox acquisition and analysis for electron tomography, J. Struct. Biol., 149, 227, 10.1016/j.jsb.2004.10.006 Nickell, 2003, Pyrodictium cannulae enter the periplasmic space but do not enter the cytoplasm, as revealed by cryo‐electron tomography, J. Struct. Biol., 141, 34, 10.1016/S1047-8477(02)00581-6 Nitsch, 1998, Group II chaperonin in an open conformation examined by electron tomography, Nat. Struct. Biol., 5, 855, 10.1038/2296 Oettl, 1983, Three‐dimensional reconstruction and averaging of 50 S ribosomal subunits of Escherichia coli from electron micrographs, J. Mol. Biol., 163, 431, 10.1016/0022-2836(83)90067-0 O'Toole, 2003, Three‐dimensional organization of basal bodies from wild‐type and delta‐tubulin deletion strains of Chlamydomonas reinhardtii, Mol. Biol. Cell, 14, 2999, 10.1091/mbc.E02-11-0755 O'Toole, 2003, Morphologically distinct microtubule ends in the mitotic centrosome of Caenorhabditis elegans, J. Cell Biol., 163, 451, 10.1083/jcb.200304035 Penczek, 1994, The ribosome at improved resolution: New techniques for merging and orientation refinement in 3D cryo‐electron microscopy of biological particles, Ultramicroscopy, 53, 251, 10.1016/0304-3991(94)90038-8 Penczek, 1995, Double‐tilt electron tomography, Ultramicroscopy, 60, 393, 10.1016/0304-3991(95)00078-X Penczek, 1992, Three‐dimensional reconstruction of single particles embedded in ice, Ultramicroscopy, 40, 33, 10.1016/0304-3991(92)90233-A Provencher, 1988, Three‐dimensional reconstruction from electron micrographs of disordered specimens. I. Method, Ultramicroscopy, 25, 209, 10.1016/0304-3991(88)90016-2 Radermacher, 1992, Weighted back‐projection methods Radermacher, 1986, A new 3D reconstruction scheme applied to the 50S ribosomal subunit of Escherichia coli, J. Microsc., 141, RP1, 10.1111/j.1365-2818.1986.tb02693.x Radermacher, 1987, Three‐dimensional reconstruction from single‐exposure random conical tilt series applied to the 50S ribosomal subunit of Eschericia coli, J. Microsc., 146, 113, 10.1111/j.1365-2818.1987.tb01333.x Radon, 1917, Über die Bestimmung von Funktionen durch ihre Integralwerte längs gewisser Mannigfaltigkeiten. Berichte Sächsische Akadamie der Wissenschaften, Leipzig, Math.‐Phys. Kl., 69, 262 Rath, 2003, Fast 3D motif search of EM density maps using a locally normalized cross‐correlation function, J. Struct. Biol., 144, 95, 10.1016/j.jsb.2003.09.029 Saxberg, 1981, Quantum noise in 2D projections and 3D reconstructions, Ultramicroscopy, 6, 85, 10.1016/S0304-3991(81)80182-9 Saxton, 1982, The correlation averaging of a regularly arranged bacterial cell envelope protein, J. Microsc., 127, 127, 10.1111/j.1365-2818.1982.tb00405.x Schatz, 1995, Structure of Lumbricus terrestris hemoglobin at 30 Å resolution determined using angular reconstitution, J. Struct. Biol., 114, 28, 10.1006/jsbi.1995.1003 Scheres, 2005, Maximum‐likelihood multi‐reference refinement for electron microscopy images, J. Mol. Biol., 348, 139, 10.1016/j.jmb.2005.02.031 Sigworth, 1998, A maximum‐likelihood approach to single‐particle image refinement, J. Struct. Biol., 122, 328, 10.1006/jsbi.1998.4014 Steinbrecht, 1987, Freeze‐substitution and freeze drying Stewart, 2004, Noise bias in the refinement of structures derived from single particles, Ultramicroscopy, 102, 67, 10.1016/j.ultramic.2004.08.008 Stoffler, 2003, Cryo‐electron tomography provides novel insights into nuclear pore architecture: Implications for nucleocytoplasmic transport, J. Mol. Biol., 328, 119, 10.1016/S0022-2836(03)00266-3 Subramaniam, 2005, Bridging the imaging gap: Visualizing subcellular architecture with electron tomography, Curr. Opin. Microbiol., 8, 316, 10.1016/j.mib.2005.04.012 Taylor, 1999, Tomographic 3D reconstruction of quick‐frozen, Ca2+‐activated contracting insect flight muscle, Cell, 99, 421, 10.1016/S0092-8674(00)81528-7 van Heel, 1987, Angular reconstitution: A posteriori assignment of projection directions for 3D reconstructions, Ultramicroscopy, 21, 111, 10.1016/0304-3991(87)90078-7 van Heel, 2000, Single‐particle electron cryo‐microscopy: Towards atomic resolution, Q. Rev. Biophys., 33, 307, 10.1017/S0033583500003644 van Heel, 1992, Correlation function revisited, Ultramicroscopy, 46, 307, 10.1016/0304-3991(92)90021-B Vogel, 1988, Three‐dimensional reconstruction from electron micrographs of disordered specimens. II. Implementation and results, Ultramicroscopy, 25, 223, 10.1016/0304-3991(88)90017-4 Wagenknecht, 2002, Electron tomography of frozen‐hydrated isolated triad junctions, Biophys J., 83, 2491, 10.1016/S0006-3495(02)75260-0 Walz, 1998, 26S proteasome structure revealed by three‐dimensional electron microscopy, J. Struct. Biol., 121, 19, 10.1006/jsbi.1998.3958 Walz, 1997, Tricorn protease exists as an icosahedral supermolecule in vivo, Mol. Cell, 1, 59, 10.1016/S1097-2765(00)80007-6 Walz, 1997, Electron tomography of single ice‐embedded macromolecules: Three‐dimensional alignment and classification, J. Struct. Biol., 120, 387, 10.1006/jsbi.1997.3934 Winkler, 2003, Focus gradient correction applied to tilt series image data used in electron tomography, J. Struct. Biol., 143, 24, 10.1016/S1047-8477(03)00120-5 Yang, 2005, Unified 3‐D structure and projection orientation refinement using quasi‐Newton algorithm, J. Struct. Biol., 149, 53, 10.1016/j.jsb.2004.08.010 Zheng, 2004, An improved strategy for automated electron microscopic tomography, J. Struct. Biol., 147, 91, 10.1016/j.jsb.2004.02.005