- Cryo-EM images molecules frozen in vitreous ice at near-atomic resolution.
- The technique bypasses crystallography's requirement for protein crystals.
- Resolution reached 1.22 angstroms in 2020, matching X-ray crystallography.
Cryo-electron microscopy (cryo-EM) is a structural biology technique that images biological molecules frozen in a thin layer of vitreous ice, preserving their natural shape and producing three-dimensional structures at near-atomic resolution.
Why It Matters
Key figure
1.22 u00c5
Resolution record for cryo-EM, set in 2020 using apoferritin
Structural biologists spent decades relying on X-ray crystallography to map proteins and other biomolecules. That method requires growing crystals, a process that excludes many important targets. Membrane proteins, large flexible complexes, and molecules that resist crystallization remained out of reach.
Cryo-EM bypasses that limitation entirely. It images molecules in solution, frozen so rapidly that water forms glass rather than ice crystals.
Since the early 2010s, improvements in electron detectors have pushed cryo-EM resolution from blurry blobs to individual atoms. The technique now accounts for a growing share of new protein structures deposited in the Protein Data Bank.
The practical consequences are direct. Pharmaceutical companies use cryo-EM to visualize drug targets that crystallography cannot handle, including G-protein-coupled receptors (GPCRs), the target class for roughly 35% of approved drugs. During the COVID-19 pandemic, cryo-EM structures of the SARS-CoV-2 spike protein guided vaccine and antiviral design within weeks of the virus's emergence.
How It Works
A few microliters of purified protein solution are applied to a metal grid coated with a thin carbon film. Filter paper blots away most of the liquid, leaving a layer less than 100 nanometers thick. The grid is then plunged into liquid ethane cooled to around -180 degrees Celsius.
Key figure
2017
Nobel Prize in Chemistry awarded for cryo-EM development
The cooling happens fast enough (more than 100,000 degrees per second) to prevent water molecules from arranging into crystals. Instead, the water vitrifies: it solidifies into an amorphous, glass-like state that preserves the protein in its native conformation. Jacques Dubochet, then a group leader at the European Molecular Biology Laboratory (EMBL) in Heidelberg, developed this vitrification method in the early 1980s.
An electron beam then passes through the frozen sample. Because biological molecules are sensitive to radiation, the beam is kept weak, producing noisy images. Each image captures a two-dimensional projection of a single molecule in a random orientation.
Software developed by Joachim Frank, then at the Wadsworth Center of the New York State Department of Health, classifies tens of thousands to millions of these projections by viewing angle. The software averages them to build a three-dimensional reconstruction.
Richard Henderson, at the MRC Laboratory of Molecular Biology in Cambridge, first used electron microscopy to determine the structure of the membrane protein bacteriorhodopsin at 7-angstrom resolution in 1975. By 1990, he had pushed the technique to atomic resolution, proving that electron microscopy could match X-ray crystallography for biological specimens. Henderson, Frank, and Dubochet shared the 2017 Nobel Prize in Chemistry for their combined contributions.
Key Context
The "resolution revolution" arrived around 2013 with direct electron detectors, which capture electrons more efficiently than the photographic film and CCD cameras used previously. Before this advance, cryo-EM rarely resolved features smaller than about 10 angstroms.
By 2020, two groups independently broke the 1.5-angstrom barrier using the test protein apoferritin. The MRC team reached 1.22 angstroms. A team led by Holger Stark at the Max Planck Institute for Biophysical Chemistry in Gottingen reached 1.25 angstroms, resolving individual atoms within a protein for the first time.
Cryo-EM and X-ray crystallography are complementary rather than competing methods. Crystallography still excels at high-throughput screening of small-molecule drug candidates bound to a single protein target. Cryo-EM is better suited for large, flexible, or membrane-embedded complexes and for capturing multiple conformational states of the same molecule in a single experiment.
FAQ
What is the difference between cryo-EM and traditional electron microscopy?
Traditional electron microscopy requires samples to be chemically fixed, dehydrated, and often stained with heavy metals, which can distort molecular structures. Cryo-EM preserves samples in vitreous ice at cryogenic temperatures, maintaining their native hydrated state. This eliminates staining artifacts and allows imaging of molecules as they exist in solution.
Can cryo-EM determine structures as precisely as X-ray crystallography?
Yes, for certain targets. Cryo-EM has achieved resolutions below 1.5 angstroms on favorable samples like apoferritin, comparable to the best crystallographic results. However, crystallography still reaches higher resolution more routinely for small, rigid proteins that form well-ordered crystals.
Why did cryo-EM win a Nobel Prize?
The 2017 Nobel Prize in Chemistry recognized Jacques Dubochet, Joachim Frank, and Richard Henderson for foundational contributions spanning four decades. Dubochet solved the vitrification problem, Frank developed computational methods for 3D reconstruction from noisy images, and Henderson proved electron microscopy could achieve atomic resolution on biological specimens.
How is cryo-EM used in drug discovery?
Pharmaceutical researchers use cryo-EM to visualize drug targets that resist crystallization, particularly membrane proteins like GPCRs and ion channels. The technique reveals how candidate molecules bind to their targets, guiding medicinal chemistry optimization. It also captures multiple conformational states, showing how drugs alter protein behavior.
Related Reading
Sources
- Primary Research:
- Atomic-resolution protein structure determination by cryo-EM (Nakane et al., Nature 587, 2020)
- Single-particle cryo-EM at atomic resolution (Yip et al., Nature 587, 2020)
- Additional Context:
- The Nobel Prize in Chemistry 2017 - Press Release (nobelprize.org)
- Cryo-electron microscopy breaks the atomic resolution barrier at last (Science, 2020)
- Developments, applications, and prospects of cryo-electron microscopy (Cheng et al., PMC, 2020)
Fact Check: Claim-by-Claim Verification Verified
All eight core claims verified against primary sources. No corrections required. GPCR 35% figure confirmed by Hauser et al. (2018); resolution records confirmed by Nature publications (2020).
Sources used for verification
- Nobel Prize in Chemistry 2017 Press Release - nobelprize.org
- Nakane et al. (2020) - nature.com
- Yip et al. (2020) - nature.com
- Hauser et al. (2018) - pmc.ncbi.nlm.nih.gov
- EMBL Nobel announcement - embl.org
