Single-Particle Cryo-EM: What happens inside the Black Box?

Electron microscopy has been an important method for visualising biological structures and processes since the 1940s. The discovery of a practical vitreous-ice specimen-preparation technique in the mid-1980s [Adrian 1984] led to modern-day Cryogenic Electron Microscopy (Cryo-EM) which in recent years has become a major technique for studying the architecture of biological macromolecules. Many further instrumental and data-analysis improvements were established in the decades after the introduction of the “vitreous-ice” state of water. Especially the advent of direct electron detectors boosted the quality of the recorded data, allowing atomic-resolution information of biological complexes to be harvested in the early 2010s, developments that truly revolutionized the use of Cryo-EM in structural biology. Single-Particle Analysis (SPA) of isolated molecules, prepared in a thin layer of vitreous water, has proven a most successful approach in structural biology and now often supplants the use of classical techniques like X-ray crystallography, especially for large biological complexes. The ever-increasing number of researchers using Cryo-EM is reflected by the growing number of depositions in the Electron Microscopy Data Bank (EMDB). Explaining this methodology to a new generation of researchers has now become a priority. In writing this review we were reminded of some persistent confusions that emerged in the early days of Cryo-EM but that continue to muddle the field. A new problem with the prolific use of Graphic User Interfaces (GUIs), is that the underlying methodology is often no longer transparent to the users of these “black boxes”. Complicated procedures, well hidden behind a GUI window, may contain methodological flaws that the user must be aware of. The conquering of markets in this booming Cryo-EM field – crucial for developing new pharmaceuticals – must not prevail over scientific integrity. We here describe and critically review the principles of single-particle Cryo-EM. We warn for procedures that have gone astray and could generate serious problems especially in the quality-control of Single-Particle Cryogenic Electron Microscopy.