National Center for Biotechnology: The electron cryomicroscope that sees the secrets of life

In the labyrinthine basement of the National Center for Biotechnology (CNB-CSIC), laboratories full of instruments are distributed where personnel in lab coats work concentrated at their desks. A room at the end of the tour breaks the harmony of flasks and pipettes. It is a large room with numerous screens and computers. Before some of them, controls that look like a spaceship. They are the controls of the precious treasure that is hidden in the next room: two electronic cryomicroscopes that allow the research staff to know the three-dimensional structure of proteins and viruses.

These huge devices, up to three meters high, use electrons instead of light while keeping samples at cryogenic temperatures of almost -200 °C to capture images with atomic resolution. The last to be inaugurated, last May and with the then minister Pedro Duque as master of ceremonies, is the most advanced in our country and involved an investment of 8 million euros.

The National Center for Biotechnology has opened the first two units in Spain in 2021

Since molecular biology was born, attempts have been made to determine the three-dimensional structure of biomolecules. Proteins or nucleic acids present a characteristic spatial organization that has to do with their function. Thus, work has been done on the development of techniques that allow knowing its shape. First came X-ray diffraction or crystallography.

The images obtained by Rosalind Franklin with this technique allowed James Watson and Francis Crick to propose the double helix structure of DNA. Then came nuclear magnetic resonance. Finally, the electron cryomicroscope established itself as the most powerful technique for revealing the structures of molecules and, therefore, their functions.

The process of obtaining data with this tool supposes an art of preparation, knowledge and a lot of pulse. The CNB’s electron cryomicroscopy service is in charge of this, which is the Spanish node of the European network of scientific infrastructures Instruct.

A technician works with an electron microscope at the National Center for Biotechnology (CNB-CSIC)


These artisans of the invisible have the double task of keeping the equipment operational and advising the scientists who have requested the use of the devices. “Techniques like ours require a lot of experience and work, and new users don’t have to spend years learning to implement them,” says Francisco Javier Chichón, a member of the service directed by Rocío Arranz.

With the use of electrons, much higher resolutions are achieved than those achieved by optical microscopes. These particles travel with very short wavelengths, making it possible to distinguish two points that are very close together. But they have a problem facing the study of biomolecules.

“Biological molecules have grown three-dimensionally through very weak bonds. We cannot mistreat them”, says José María Valpuesta, head of the Department of Macromolecular Structures and scientific director of the electron cryomicroscopy service. “If electrons were irradiated directly at them in the electron microscope, these bonds would be rapidly destroyed.”

The electron microscopy technique has been recognized with a Nobel Prize for having transformed the study of proteins

The importance of cryoelectron microscopy has been recognized with a Nobel Prize. Specifically, the 2017 Chemistry Prize, which was awarded to Jacques Dubochet for the development of vitrification. Along with him, Joachim Frank and Richard Henderson received the award for the implementation of cryoelectron microscopy.

The vitrification process consists of freezing samples at such a speed that the water present in them does not have time to form ice crystals. Otherwise, the electrons could not pass through it and the biological structures would be destroyed.

In a room within the cryomicroscopy service, Noelia Zamarreño, a laboratory technician, has everything ready to carry out the process. With very fine tweezers, grab a circular grid three millimeters in diameter. This consists of a metal framework covered with a thin layer of carbon. It hooks it onto a robot that will carry out the process in a semi-automated way and deposits a drop of the solution on it where the biomolecules to be studied float. Like a kingfisher, the apparatus launches the grid into liquid ethane which immediately turns the sample into icy glass.

Seen from the outside, an electron microscope looks like a huge refrigerator.

Seen from the outside, an electron microscope looks like a huge refrigerator.


A liquid nitrogen tank will then keep the complex at about -180°C until future observation. It will take thousands of captures – they are actually bursts called movies – taken for hours to reveal the three-dimensional structures. The “photographs” will be taken in the vacuum generated inside the electron cryomicroscope to prevent electrons from interacting with matter and being diverted.

One floor above, the Biocomputing Unit develops equations and algorithms to reveal the organization of atoms from collections of images made up of white, black and gray pixels.

“We take care of information processing issues,” says José María Carazo, who runs the department together with Carlos Óscar Sorzano. Their work is essential not only to find ways in the middle of the noise but also to analyze in parallel to the data collection if said process is being carried out correctly.

Leyre Flamarique has received a CSIC-BBVA Grant for Scientific Communication

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National Center for Biotechnology: The electron cryomicroscope that sees the secrets of life