Broadening access to cryoEM through centralized facilities

Abstract

Cryogenic electron microscopy (cryoEM) uses images of frozen hydrated biological specimens to produce macromolecular structures, opening up previously inaccessible levels of biological organization to high-resolution structural analysis. CryoEM has the potential for broad impact in biomedical research, including basic cell, molecular, and structural biology, and increasingly in drug discovery and vaccine development. Recent advances have led to the expansion of molecular and cellular structure determination at an exponential rate. National and regional centers have emerged to support this growth by increasing the accessibility of cryoEM throughout the biomedical research community. Through cooperation and synergy, these centers form a network of resources that accelerate the adoption of best practices for access and training and establish sustainable workflows to build future research capacity.

Keywords: automation; biophysics education; cryogenic electron microscopy (cryoEM); structural biology; training.

Figure 1:. A centralized control room provides an environment for efficient collaboration.

As an example, the Simons Electron Microscopy Center (SEMC) has two control rooms that provide remote microscope operation. Pictured here is the control room where operators and users collect data on four dedicated National Center for CryoEM Access and Training (NCCAT) Krios microscopes and a Glacios microscope, and the dedicated National Center for In-situ Tomographic Ultramicroscopy (NCITU) Aquilos2 focused ion beam-scanning electron microscope (FIB-SEM). Each microscope station comprises microscope, camera, and data collection computers. There is also open desk space for an embedded engineer and open seating for researchers, staff, or trainees to comfortably sit together for discussions. This arrangement keeps experienced help close to every data collector. Adjacent to the control room, behind blue doors, are microscope rooms and a dehumidified room for sample preparation and autoloader grid handling.

Figure 2:. CryoEM resources provide access to instrumentation.

We identified 49 centers, after soliciting information from the cryoEM community, marked with blue dots, that provide general access to cryoEM instrumentation. We acknowledge that this is not a comprehensive list, but it includes many of the world’s currently largest centers: the 4 National Institutes of Health (NIH) centers in the United States, 11 iNEXT consortium sites in Europe and the United Kingdom, as well as Electron Bio-Imaging Centre (eBIC) and Southern University of Science and Technology (SUSTech) in China. National facilities have also been established in Australia and India, and South America has one cryoEM capable microscope located in Brazil. The geographical distribution of resources is uneven, but large centers can provide access if researcher can ship samples for analysis. A list of cryoEM instrumentation centers with links to websites is available.

Box 1, Figure I:

Many structures of SARS-CoV-2 proteins were determined using data collected at National Center for CryoEM Access and Training (NCCAT) in 2020. These include A) the S-protein bound to antibody fragments (EMDB: 22156), B) and C) the S-protein under different experimental conditions (EMDB: 22001, 21999), D) S-protein with a D614G mutation (EMDB: 22826) E) the S-protein bound to the ACE2 receptor (EMDB: 22941), and F) the viral replication-transcription complex (EMDB: 22160).

Box 2, Figure I:

Merit badges are modular training units organized in three focus areas (top), and each badge is a standalone qualification. Here, we highlight one example of a sample preparation merit badge for use of a Vitrobot plunge freezing instrument (middle). The requirements completed by trainees include testing of base knowledge with a quiz (links to relevant training resources are provided), followed by hands-on training that includes supervised practice and demonstration of competent independent use. Location specific details are separated from a standardized standard operating procedure that can be used at any center.