Plunging into Cryo-EM: Precision Sample Prep for Structural Success

Cryo-EM offers unprecedented insights into complex macromolecules, but success is dependent on the quality of your sample. At Sygnature Discovery, we’ve built a precision-focused cryo-EM lab to ensure your structural biology project starts with the best possible sample.

Expertise in Protein Production for Structural Biology

Sygnature Protein Science has a strong track record of producing proteins for structural studies, including:

• A wide range of membrane proteins.
• Large, multi-component protein complexes.
• Protein:nucleic acid complexes
• Proteins that are difficult to express, purify, or stabilize.

Our experience ensures that your cryo-EM project starts with the best possible sample—setting the stage for successful structure determination.

Figure 1. Our Cryo-EM Workflow: From Gene to Structure. We offer a fully integrated cryo-EM pipeline, streamlined approach eliminates delays and preserves sample integrity.

Why Precision Purification Matters for Cryo-EM

Electron cryo-microscopy (cryo-EM) continues to transform structural biology, offering unprecedented insights into complex macromolecules. Much of the value in cryo-EM lies in visualising proteins or protein-states that are otherwise unobtainable—particularly large, flexible, and/or membrane proteins that are often unsuitable for study by other structural techniques.

Protein quality is most often the determining factor in achieving successful structural biology projects. Precision purification and careful handling of difficult samples are essential to harness the full potential of cryo-EM, especially as the technique pushes the limits of what can be visualised.

There is an argument to be made for lower protein purity requirements for cryo-EM, since particles of interest can be purified from a milieu of contaminants in silico. While this is true, the structure determination process is much more robust if particles are isolated before being applied to a grid—rather than searching for a ‘needle in a haystack’ computationally. Additionally, for compound or fragment screening by cryo-EM, a robust apo form of the sample is a desired starting point to allow for high throughput.

Unstable proteins may degrade quickly, requiring rapid transfer from the final purification step to grid preparation. Large protein complexes may purify as mixtures of components, needing precise separation to yield samples with the desired combination. A successful, robust cryo-EM workflow relies on:

• Sample homogeneity
• Often high protein concentration (~5 mg/mL)
• Detergent and buffer composition that maintains protein stability but is not detrimental to particle signal
• Limited levels of contaminants or aggregation

Even the smallest loss of resolution due to sample quality can mean the difference between an interpretable structure and “blobology.” It is essential that purification steps are optimised before a sample is applied to a grid. At Sygnature Discovery, our AKTA Micro system offers a significant upgrade in precision, sensitivity, and sample integrity compared to standard systems—ensuring your cryo-EM project starts with the best possible sample.

Meeting the Challenge: Our Cryo-EM Prep Lab

To meet the precision purification needs outlined above, Sygnature Discovery has built a dedicated cryo-EM sample preparation lab designed to handle unstable, low-volume, and complex protein samples with care and efficiency.

A key part of this set-up is the AKTA Micro system, optimised for small-volume, high-resolution purification. It features micro tubing (0.13 mm diameter), high-sensitivity UV detection, and minimal internal dead volumes, ensuring accurate quantification and minimal sample loss. The fraction collector is fitted with a micronozzle to dispense droplets as small as 7.5 μL, allowing the most monodisperse fractions to be applied directly onto 2–3 cryo-EM grids.

Co-located with the AKTA Micro is our Vitrobot IV, a plunge-freezing device that vitrifies samples in liquid ethane. This rapid freezing aims to preserve native protein conformations and prevents ice crystal formation, ensuring optimal particle quality for imaging.

By placing these systems side-by-side, we eliminate delays between purification and grid preparation, critical for unstable proteins, and give every cryo-EM project the best possible chance of success.

Figure 2. Cryo-EM Sample Preparation Lab Setup, from planning with blocks to reality. Left: model of our cryo-EM prep lab, Right: Our cryo-EM prep lab

Industry standard grid preparation with the Vitrobot IV

The Vitrobot IV is a plunge-freezing device that performs the critical cryo-fixation step, immediately vitrifying samples in coolant . This rapid freezing preserves native protein conformations and prevents ice crystal formation, which can compromise particle visibility and quality.

Co-locating the Vitrobot IV with our AKTA Micro purification system eliminates delays between purification and grid preparation, critical for unstable proteins, and ensures that fractions containing homogeneous sample at appropriate concentration are vitrified immediately. This setup gives every cryo-EM project the best possible chance of success.

Benchmarking our AKTA Micro

To really put our AKTA Micro to the test, we did side-by-side purification of the Cereblon:DDB1 complex using a Superdex 200 3.2/300 column. The complex was purified by analytical size-exclusion chromatography (aSEC) using our standard aSEC set up on an AKTA Go system or using our AKTA Micro system.

Sharper and More Symmetrical Peaks

When loading samples using a complete loop fill (100 µL sample loaded into 50 µL loop), we saw that the AKTA Micro gave a sharper and more symmetrical peak than the AKTA Go. This was also true for partial loop filling. We demonstrated that when sample is limited, a partial loop fill (25 µL in a 50 µL loop) still allowed us to retain the sharp defined peaks on the AKTA Micro.

Figure 3. aSEC analysis using a complete loop fill (100µL load in a 50µL loop)

Figure 4. aSEC analysis using a partial loop fill (25µL load in a 50µL loop)

Better resolution and peak separation

To test the AKTA Micro’s improved resolution and separation of protein mixtures, we loaded a mix of SEC standards (Ferritin – 474 kDa, Aldolase – 160 kDa, Conalbumin – 76 kDa, RNase – 13.7 kDa) onto a Superdex 200 3.2/300 column using both the AKTA Micro and AKTA Go aSEC set up.

The AKTA Micro resulted in superior separation between the eluted protein peaks ensuring higher final sample purity. The improved resolution also enables a more accurate approximation of target protein molecular weight when compared with molecular weight standards.

Figure 5. aSEC analysis of molecular weight standards (Superdex 200 3.2/300)

Concentration retention

When making cryo-EM grids, 2-4 µL of sample at ~5 mg/mL is a good aim. Often this can be a challenge with difficult to express and purify proteins, therefore, minimising sample loss is essential. Concentrating samples using centrifugal devices can not only lead to sample loss but also aggregation; even small clusters of aggregated protein can mask out single particles when viewed under an electron microscope.

The smaller tubing diameter and reduced component void volumes of the AKTA Micro minimise protein dilution. Additionally, the AKTA Micro can collect fractions of just 10 μL, whereas the AKTA Go smallest consistent fraction size is 40 μL which can dilute the peak fractions significantly.

We tested the AKTA Micro’s concentration retention by comparing the A280 measurement of the load sample to the aSEC peak fraction. For this experiment Cereblon:DDB1 was loaded at 9.1 mg/mL. The AKTA Go showed a concentration retention of only 25.3% for the full loop fill and 7.7% for the half fill. The AKTA Micro had significantly improved concentration retention of 52.9% for the full loop fill and 34.1% for the half fill.

Additionally, the small diameter tubing allows the resolution to be maintained from the post-column UV detector to the fraction collector. To show this we compared the estimated peak fraction concentration, determined by AKTA Evaluate software based on the measured A280, to the measured A280 of the collected fraction by our Denovix.

The AKTA Micro shows more accurate A280 measurements, so that additional measurements may not need to be taken, preserving precious microlitres. With more precise peak fractionation and smaller fraction sizes, allows your grids to be made with only the most concentrated and homogenous portions of the elution profile.

On-Site Grid Preparation: No Shipping, No Stress

Shipping samples for grid preparation can be detrimental—especially for unstable proteins. Delays, freeze-thaw, and/or temperature fluctuations can compromise sample quality. Our AKTA Micro and Vitrobot IV are co-located, allowing immediate transfer from final purification step to grid making. This proximity:

• Preserves sample stability, providing the best chance of project success.
• Reduces risk of aggregation or degradation.
• Enables rapid turnaround for screening and data collection.

For clients interested in freeze-thaw stability, we can explore protocols to assess how your sample behaves under cryo-storage conditions—helping you make informed decisions about long-term sample handling. Once the sample has been applied to the grid and plunged into liquid ethane to achieve fast freezing (vitreous ice), the grid is then maintained at liquid nitrogen levels and transported to a cryo-EM facility where the frozen grid is transferred into the microscope. Once frozen on the grid, there is no deterioration of the sample until it is exposed to the electron beam within the microscope.

Scalable Data Processing on AWS

Once grids are prepared and shipped to our partner facilities, we screen and collect data where appropriate. We then securely transfer the data, and process  using secure, scalable GPU clusters on AWS. This allows for parallel processing of multiple datasets and rapid structure determination. To complete your project, we also build, and real-space refine an atomic coordinate model into your map, for ease of interpretation.

Partner with Us for Cryo-EM Success

From construct design to structure refinement, our cryo-EM workflow is built to support project success. Whether you’re working with membrane proteins, large complexes, or other challenging targets, we offer a full-service solution tailored to your needs. The AKTA Micro system offers significant advantages over the AKTA Go for advancing samples for cryo-EM studies, particularly in the context of handling precious, low-volume protein samples. Producing sharper and more symmetrical chromatographic peaks. By utilizing our AKTA Micro situated directly next to our Vitrobot IV we can support your cryo-EM projects giving you the best possible chance of project success.

References

1. Rappsilber, J. (2018). Capturing protein–protein interactions in vitro and in vivo by crosslinking mass spectrometry. Analytical and Bioanalytical Chemistry, 410, 249–250.
2. Schopper, S., Kahraman, A., & Herzog, F. (2017). Complex perturbation analysis (ComPA): A method for evaluating the specificity of protein–protein interactions in SILAC-based mass spectrometry. Protein Science, 26(1), 112–119.