Preparation of High-Temperature Sample Grids for Cryo-EM

Summary

This paper provides a detailed protocol for preparing sample grids at temperatures as high as 70 °C, prior to plunge freezing for cryo-EM experiments.

Abstract

The sample grids for cryo-electron microscopy (cryo-EM) experiments are usually prepared at a temperature optimal for the storage of biological samples, mostly at 4 °C and occasionally at room temperature. Recently, we discovered that the protein structure solved at low temperature may not be functionally relevant, particularly for proteins from thermophilic archaea. A procedure was developed to prepare protein samples at higher temperatures (up to 70 °C) for cryo-EM analysis. We showed that the structures from samples prepared at higher temperatures are functionally relevant and temperature dependent. Here we describe a detailed protocol for preparing sample grids at high temperature, using 55 °C as an example. The experiment made use of a vitrification apparatus modified using an additional centrifuge tube, and samples were incubated at 55 °C. The detailed procedures were fine-tuned to minimize vapor condensation and obtain a thin layer of ice on the grid. Examples of successful and unsuccessful experiments are provided.

Introduction

The cryo-EM technology for solving the structures of protein complexes has continued to improve, particularly in the direction of obtaining high-resolution structures^1,2. In the meantime, the landscape of its application has also been expanded by varying the sample conditions such as pH or ligands prior to the vitrification process³, which involves the preparation of sample grids followed by plunge freezing^4,5. Another important condition is the temperature. Although cryo-EM experiments, like X-ray crystallography, are performed....

Protocol

NOTE: This protocol aims to use a modified commercial vitrification apparatus to prepare the cryo-electron microscopy (cryo-EM) samples at specific temperatures, especially higher than 37 °C. The overall experimental setup is shown in Figure 1. The protocol uses 55 °C as an example. For the specific conditions at other temperatures, please refer to Supplementary Table 2 in reference¹².

1. Preparation of the vitrification apparatus

1. Make a 1 cm hole in a 50 mL centrifuge tube on its closed end.
2. Place the tube in the vitrification apparatus chamber at the ult....

Results

The low magnification overview is shown in Figure 5A,B. Panel A is an example of a successful grid. There is an ice gradient from top left (thicker) to bottom right (thinner or empty). Such a grid makes it easier to find an appropriate thickness of the ice layer in the middle area suitable for data collection, such as the blue and green boxes. The grid B is too dry. The squares in the grid have bright contrast, which means that the ice layer is too thin or there is no ice la.......

Discussion

In step 1 of the protocol, make sure that the centrifuge tube has been installed well and does not fall when the experiment is in progress. Due to the accumulation of a large number of water droplets in the chamber, which could change the adsorption capacity of the filter paper, it is recommended that the overall time of the experiment should not exceed 30 min after the vitrification apparatus chamber reached the equilibration temperature. If the operation time exceeds 30 min, the operator needs to replace the filter pap.......

Materials

Name	Company	Catalog Number	Comments
Falcon tube	Falcon	352070	size: 50 mL
Filter paper	Ted Pella	47000-100	Ø55/20mm, Grade 595
HI1210	Leica		water bath
K100X	Electron Microscopy Sciences		glow discharge
Quantifoil, 1.2/1.3 200Mesh Cu grid	Ted Pella	658-200-CU-100
Titan Krios G3	Thermo Fisher Scientific	1063996	low dose imaging
Vitrobot Mark IV	Thermo Fisher Scientific	1086439
Vitrobot Tweezer	Ted Pella	47000-500