1.Introduction / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio -- 2.Features in a Subnanometer Resolution Density Map / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio -- 3.Tools: Analyzing a Subnanometer Resolution Density Map / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio -- 4.Protocol: From Density Map to Atomic Model / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio -- 5.Case Study: Mm-cpn / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio -- 6.Discussion / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio -- Acknowledgments / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio -- References / Matthew L. Baker / Mariah R. Baker / Corey F. Hryc / Frank DiMaio -- 1.Introduction / Niels Volkmann -- 2.Noise Reduction / Niels Volkmann -- 3.Segmentation / Niels Volkmann -- 4.Detection and Mapping of Macromolecular Assemblies / Niels Volkmann -- 5.Classification and Averaging / Niels Volkmann -- 6.Validation / Niels Volkmann -- Acknowledgments / Niels Volkmann -- References / Niels Volkmann -- 1.Introduction / Friedrich Förster / Elizabeth Villa -- 2.The Problem of Placing Assembly Subunits into Cryo-EM Maps / Friedrich Förster / Elizabeth Villa -- 3.Structure Prediction of Subunits / Friedrich Förster / Elizabeth Villa -- 4.Protein[-]Protein Interaction Data / Friedrich Förster / Elizabeth Villa -- 5.Model Building of a Complex Using Cryo-EM and Additional Data / Friedrich Förster / Elizabeth Villa -- 6.Refinement of Atomic Models Using High-Resolution Maps / Friedrich Förster / Elizabeth Villa -- 7.Conclusion and Outlook / Friedrich Förster / Elizabeth Villa -- References / Friedrich Förster / Elizabeth Villa -- 1.Introduction / Catherine L. Lawson -- 2.EM Structural Data Archives / Catherine L. Lawson -- 3.Deposition and Content / Catherine L. Lawson -- 4.Access / Catherine L. Lawson -- 5.Examples of Use / Catherine L. Lawson -- 6.Future Prospects / Catherine L. Lawson -- 7.Guide to Deposition of EM Structural Data / Catherine L. Lawson -- Acknowledgments / Catherine L. Lawson -- References / Catherine L. Lawson -- 1.Electron Crystallography / Andreas D. Schenk / Richard K. Hite / Andreas Engel / Yoshinori Fujiyoshi / Thomas Walz -- 2.Contributions of Electron Crystallography to the Structural Biology of Aquaporins / Andreas D. Schenk / Richard K. Hite / Andreas Engel / Yoshinori Fujiyoshi / Thomas Walz -- 3.Contributions of Structural Studies on Aquaporins to Advances in Electron Crystallography / Andreas D. Schenk / Richard K. Hite / Andreas Engel / Yoshinori Fujiyoshi / Thomas Walz -- Acknowledgments / Andreas D. Schenk / Richard K. Hite / Andreas Engel / Yoshinori Fujiyoshi / Thomas Walz -- References / Andreas D. Schenk / Richard K. Hite / Andreas Engel / Yoshinori Fujiyoshi / Thomas Walz -- 1.Introduction: The Role of Electron Microscopy in Tubulin Studies / Kenneth H. Downing / Eva Nogales -- 2.Tubulin Studies by Electron Crystallography / Kenneth H. Downing / Eva Nogales -- 3.Microtubule Structure / Kenneth H. Downing / Eva Nogales -- 4.Structure of Microtubule Assembly/Disassembly Intermediates / Kenneth H. Downing / Eva Nogales -- 5.Mechanism of Kinesin Movement Along Microtubule / Kenneth H. Downing / Eva Nogales -- 6.Drug Binding Studied by Diffraction and Modeling / Kenneth H. Downing / Eva Nogales -- 7.Tomography for Larger Structures / Kenneth H. Downing / Eva Nogales -- 8.Conclusion / Kenneth H. Downing / Eva Nogales -- Acknowledgments / Kenneth H. Downing / Eva Nogales -- References / Kenneth H. Downing / Eva Nogales -- 1.Helical Crystallization of the Bacterial Integral Membrane Protein, MsbA / John Paul Glaves / Lauren Fisher / Andrew Ward / Howard S. Young -- 2.Helical Crystallization of the Sarcoplasmic Reticulum Ca2+-ATPase / John Paul Glaves / Lauren Fisher / Andrew Ward / Howard S. Young -- 3.Discussion / John Paul Glaves / Lauren Fisher / Andrew Ward / Howard S. Young -- 4.Conclusions / John Paul Glaves / Lauren Fisher / Andrew Ward / Howard S. Young -- Acknowledgments / John Paul Glaves / Lauren Fisher / Andrew Ward / Howard S. Young -- References / John Paul Glaves / Lauren Fisher / Andrew Ward / Howard S. Young -- 1.Introduction / Justus Loerke / Jan Giesebrecht / Christian M.T. Spahn -- 2.Dealing with Heterogeneity: 3D Sorting / Justus Loerke / Jan Giesebrecht / Christian M.T. Spahn -- 3.Subnanometer Multiparticle Cryo-EM of Ribosomes in Practice / Justus Loerke / Jan Giesebrecht / Christian M.T. Spahn -- 4.Interpretation / Justus Loerke / Jan Giesebrecht / Christian M.T. Spahn -- 5.Conclusions / Justus Loerke / Jan Giesebrecht / Christian M.T. Spahn -- Acknowledgments / Justus Loerke / Jan Giesebrecht / Christian M.T. Spahn -- References / Justus Loerke / Jan Giesebrecht / Christian M.T. Spahn -- 1.Electron Microscopy and the Next Frontier in Structural Biology / Edward J. Brignole / Francisco Asturias -- 2.The Catalytic Cycle of FAS Requires Conformational Changes / Edward J. Brignole / Francisco Asturias -- 3.Methods and Rationale Employed in the Conformational Analysis of FAS / Edward J. Brignole / Francisco Asturias -- 4.EM and FAS: A Versatile Tool for a Flexible Macromolecule / Edward J. Brignole / Francisco Asturias -- Acknowledgments / Edward J. Brignole / Francisco Asturias -- References / Edward J. Brignole / Francisco Asturias -- 1.Introduction / Dorit Hanein -- 2.Testing the Lamella Hypothesis / Dorit Hanein -- 3.Challenges / Dorit Hanein -- Acknowledgments / Dorit Hanein -- References / Dorit Hanein -- 1.Introduction / Friedrich Förster / Bong-Gyoon Han / Martin Beck -- 2.Data Acquisition / Friedrich Förster / Bong-Gyoon Han / Martin Beck -- 3.Templates / Friedrich Förster / Bong-Gyoon Han / Martin Beck -- 4.Template Matching / Friedrich Förster / Bong-Gyoon Han / Martin Beck -- 5.Assessment of Performance / Friedrich Förster / Bong-Gyoon Han / Martin Beck -- 6.The Spatial Proteome of L. interrogans / Friedrich Förster / Bong-Gyoon Han / Martin Beck -- 7.Outlook / Friedrich Förster / Bong-Gyoon Han / Martin Beck -- Acknowledgments / Friedrich Förster / Bong-Gyoon Han / Martin Beck -- References / Friedrich Förster / Bong-Gyoon Han / Martin Beck -- 1.Introduction / Asaf Mader / Nadav Elad / Ohad Medalia -- 2.Specimen Preparation / Asaf Mader / Nadav Elad / Ohad Medalia -- 3.Relying on Correlative Light and Electron Microscope for Cellular Structural Study of Eukaryotic Cells / Asaf Mader / Ohad Medalia / Nadav Elad -- 4.Cryoelectron Tomography of Cytoskeleton-Driven Processes / Asaf Mader / Nadav Elad / Ohad Medalia -- 5.Cryotomography of Midbodies / Asaf Mader / Nadav Elad / Ohad Medalia -- 6.Structural Analysis of the Nuclear Pore Complex by Cryo-ET / Asaf Mader / Nadav Elad / Ohad Medalia -- 7.Concluding Remarks / Asaf Mader / Nadav Elad / Ohad Medalia -- Acknowledgments / Asaf Mader / Nadav Elad / Ohad Medalia -- References / Asaf Mader / Nadav Elad / Ohad Medalia -- 1.Introduction / Jun Liu / Elizabeth R. Wright / Hanspeter Winkler -- 2.Cryoelectron Tomography / Jun Liu / Elizabeth R. Wright / Hanspeter Winkler -- 3.3D Visualization of Intact HIV Virion / Jun Liu / Elizabeth R. Wright / Hanspeter Winkler -- 4.Conclusions and Perspective / Jun Liu / Elizabeth R. Wright / Hanspeter Winkler -- Acknowledgments / Jun Liu / Elizabeth R. Wright / Hanspeter Winkler -- References / Jun Liu / Elizabeth R. Wright / Hanspeter Winkler -- 1.Introduction / Dmitry Lyumkis / Arne Moeller / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher -- 2.Specimen Preparation / Dmitry Lyumkis / Arne Moeller / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher -- 3.Autoloading and Robotic Screening / Dmitry Lyumkis / Arne Moeller / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher -- 4.Microscopy / Dmitry Lyumkis / Arne Moeller / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S.

Potter / Bridget Carragher -- 5.Image Processing / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher / Dmitry Lyumkis / Arne Moeller -- 6.Assessment and Integration / Dmitry Lyumkis / Arne Moeller / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher -- 7.The Future of Automation / Dmitry Lyumkis / Arne Moeller / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher -- Acknowledgments / Dmitry Lyumkis / Arne Moeller / Anchi Cheng / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / James Pulokas / Joel D. Quispe / Neil R. Voss / Clinton S. Potter / Bridget Carragher -- References / Arne Moeller / Dmitry Lyumkis / Bridget Carragher / Clinton S. Potter / Neil R. Voss / Joel D. Quispe / James Pulokas / Amber Herold / Eric Hou / Christopher Irving / Erica L. Jacovetty / Pick-Wei Lau / Anke M. Mulder / Anchi Cheng.