MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS,1092-2172/99/$04.00⫹0Dec. 1999, p. 862–922 Vol. 63, No. 4Copyright © 1999, American Society for Microbiology. All Rights Reserved.Adding the Third Dimension to Virus Life Cycles: Three-DimensionalReconstruction of Icosahedral Viruses fromCryo-Electron MicrographsT. S. BAKER,1* N. H. OLSON,1AND S. D. FULLER2,3Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-13921; Structural Biology Programme,European Molecular Biology Laboratory, 69117 Heidelberg, Germany2; and The Welcome Trust Centre forHuman Genetics, University of Oxford, Oxford, United Kingdom3INTRODUCTION .......................................................................................................................................................863Abbreviations used..................................................................................................................................................866THE LANGUAGE OF ICOSAHEDRAL SYMMETRY .........................................................................................866The Icosahedron......................................................................................................................................................866Triangulation Numbers..........................................................................................................................................867PREPARATION OF VITRIFIED VIRUS SAMPLES ............................................................................................869CRYO-EM OF VIRUSES...........................................................................................................................................871Search for Suitable Specimen Areas....................................................................................................................871Imaging Conditions ................................................................................................................................................871Radiation Damage ..................................................................................................................................................873Contrast Enhancement...........................................................................................................................................873IMAGE ANALYSIS AND 3D RECONSTRUCTION .............................................................................................875Determination of Particle Orientation and Origin ............................................................................................876Common Lines and Cross-Common Lines Methods .........................................................................................876Resolution Limits....................................................................................................................................................876Selection and Digitization of Micrographs .........................................................................................................877Processing the Digitized Micrograph...................................................................................................................878Refinement of Particle Parameters and Calculation of 3D Reconstruction...................................................878Model-Based Refinement .......................................................................................................................................878CTF Correction .......................................................................................................................................................878Almost-Icosahedral Objects...................................................................................................................................879Reliability of Reconstruction.................................................................................................................................879NOT JUST A PRETTY PICTURE ...........................................................................................................................880Visualization and Representation.........................................................................................................................880Reliability of Difference Imaging (A Cautionary Note).....................................................................................881Modeling and Comparison with X-Ray Structures............................................................................................881Phasing of X-Ray Data with EM Data ................................................................................................................882VIRUS LIFE CYCLES IN THREE DIMENSIONS ...............................................................................................882Shared Features of Virus Life Cycles ..................................................................................................................882Cell Attachment ......................................................................................................................................................884HRV16-ICAM complex.......................................................................................................................................884Other cryo-EM studies concerning receptor-virus interactions...................................................................885Activation .................................................................................................................................................................885Enveloped virus entry.........................................................................................................................................885Nonenveloped virus entry ..................................................................................................................................887Release of Genome..................................................................................................................................................888Model of genome release in FHV .....................................................................................................................889Other cryo-EM studies concerning genome release.......................................................................................890Transcription and Translation
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