Name: single-particle cryo-em data collection with stage tilt using leginon
Uploaded: 2022-07-01T13:00:00
Description: Watch this Scientific Journal Video about Single-Particle Cryo-EM Data Collection with Stage Tilt using Leginon at JoVE.com

We thank Bill Anderson, Charles Bowman, and Jean-Christophe Ducom (TSRI) for help with microscopy, Leginon installations, and data transfer infrastructure. We also thank Gordon Louie (Salk Institute) and Yong Zi Tan (National University of Singapore) for the critical reading of the manuscript. We thank Chris Russo (MRC Laboratory of Molecular Biology, Cambridge) for providing us with the plasmid for expression of DPS.&#160;This work was supported by grants from the US National Institutes of Health (U54AI150472,&#160;U54 AI170855, and R01AI136680 to DL), the National Science Foundation (NSF MCB-2048095 to DL), the Hearst Foundations (to DL), and Arthur and Julie Woodrow Chair (to J. P. N.). T.S. is supported by an F32 postdoctoral fellowship from the National Institutes of Health (GM148049).

1. Sample preparation
<ol>
	<li>Use grids containing gold foil and gold grid support16 (see Table of Materials) because tilted data collection can accentuate beam-induced motion17. 
	NOTE: For the present study, samples on grids were vitrified using the manual plunging and blotting technique18 in a humidified (greater than 80%) cold room (~4 &#176;C).</li>
	<li>Avoid using grids containing copper support and c...

<ol>
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A., Gonen, T., Nannenga, B. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> cryoEM: Methods and Protocols. , 125-144 (2021).</li><li>Cash, J. N., Kearns, S., Li, Y., Cianfrocco, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-resolution+cryo-EM+using+beam-image+shift+at+200+keV.">High-resolution cryo-EM using beam-image shift at 200 keV.</a> IUCrJ. 7 (6), 1179-1187 (2020).</li><li>Peck, J. V., Fay, J. F., Strauss, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-speed+high-resolution+data+collection+on+a+200+keV+cryo-TEM.">High-speed high-resolution data collection on a 200 keV cryo-TEM.</a> IUCrJ. 9 (2), 243-252 (2022).</li><li>Bouvette, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Beam+image-shift+accelerated+data+acquisition+for+near-atomic+resolution+single-particle+cryo-electron+tomography.">Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography.</a> Nature Communications. 12 (1), 1957 (1957).</li><li>Cheng, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High+resolution+single+particle+cryo-electron+microscopy+using+beam-image+shift.">High resolution single particle cryo-electron microscopy using beam-image shift.</a> Journal of Structural Biology. 204 (2), 270-275 (2018).</li><li>Tegunov, D., Cramer, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real-time+cryo-electron+microscopy+data+preprocessing+with+Warp.">Real-time cryo-electron microscopy data preprocessing with Warp.</a> Nature Methods. 16 (11), 1146-1152 (2019).</li><li>. 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Preferred particle orientation caused by specimen adherence to the air-water interface is one of the last major bottlenecks to routine high-resolution structure determination using cryo-EM SPA4,5,6. The data collection scheme presented here provides an easy-to-implement strategy for improving the orientation distribution of particles within a dataset. We note that the protocol requires no additional equipment or software and doe...

The advent of direct electron detectors over the past decade1,2,3 has spurred an exponential increase in the number of high-resolution structures of macromolecules and macromolecular assemblies solved using single-particle cryo-EM4,5,6. Almost all purified macromolecular species are expected to be amenable to structure determination using cryo-EM, except for the smallest proteins ~10 kDa in size or below7. The amount of starting material needed for grid preparation and structure determination is at least an order of magnitude less than other structure determination techniques, such as nuclear magnetic resonance spectroscopy and X-ray crystallography4,5,6.
However, a principal challenge for structure determination by cryo-EM involves suitable grid preparation for imaging. An extensive study evaluating diverse samples using different vitrification strategies and grids suggested that most approaches for vitrifying samples on cryo-EM grids lead to preferential adherence of macromolecules to the air-water interface8. Such adherence can potentially cause four suboptimal outcomes: (1) the macromolecular sample completely denatures, in which case no successful data collection and processing is possible; (2) the sample partially denatures, in which case it may be possible to obtain structural insights from regions of the macromolecule that are not damaged; (3) the sample retains native structure, but only one set of particle orientations relative to the direction of the electron beam are represented in the images; (4) the sample retains native structure, and some but not all possible particle orientations relative to the direction of the electron beam are represented in the images. For cases (3) and (4), tilted data collection will help with minimizing directional resolution anisotropy affecting the reconstructed cryo-EM map and provides a generalizable solution for a wide variety of samples9. Technically, tilting can also benefit case (2), since the denaturation presumably occurs at the air-water interface and similarly limits the number of distinct orientations represented within the data. The extent of orientation bias in the dataset can potentially be altered by experimenting with solution additives, but a lack of broad applicability hampers these trial-and-error approaches. Tilting the specimen stage at a single optimized tilt angle is sufficient to improve the distribution of orientations by virtue of altering the geometry of the imaging experiment9 (Figure 1). Due to the geometric configuration of the preferentially-oriented sample with respect to the electron beam, for each cluster of preferential orientations, tilting the grid generates a cone of illumination angles with respect to the cluster centroid. Hence, this spreads out the views and consequently improves Fourier space sampling and the isotropy of directional resolution.
There are, in practice, some detriments to tilting the stage. Tilting the specimen stage introduces a focus gradient across the field of view, which may affect the accuracy of contrast transfer function (CTF) estimations. Tilted data collection may also lead to increased beam-induced particle movement caused by increased charging effects when imaging tilted specimens. Grid tilting also leads to an increase in apparent ice thickness, which in turn leads to noisier micrographs and may ultimately impact the resolution of reconstructions5,9,10. It may be possible to overcome these issues by applying advanced computational data-processing schemes that are briefly described in the protocol and discussion sections. Lastly, tilting can lead to increased particle overlap, hindering the subsequent image processing pipeline. Although this can be mitigated to some extent by optimizing on-grid particle concentration, it is nonetheless an important consideration. Here, a simple-to-implement protocol is described for tilted data collection using the Leginon software suite (an automated image acquisition software), available open access and compatible with a broad range of microscopes11,12,13,14. The method requires at least version 3.0 or higher, with versions 3.3 onward containing dedicated improvements to enable tilted data collection. No additional software or equipment is necessary for this protocol. Extensive instructions on computational infrastructure and installation guides are provided elsewhere15.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Cryosparc Live v3.1.0+210216</td>
			<td>Structura Biotechnology</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>DPS protein</td>
			<td></td>
			<td></td>
			<td>Purification adapted from protocol described in K.Naydenova et al IUCrJ. 2019 Nov 1; 6(Pt 6): 1086&#8211;1098.</td>
		</tr>
		<tr>
			<td>K2 Summit Direct Electron Detector</td>
			<td>Gatan</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Leginon software suite</td>
			<td></td>
			<td></td>
			<td>C Suloway et al Journal of Structural Biology 151 (1): pp. 41-60.</td>
		</tr>
		<tr>
			<td>Manual plunging device</td>
			<td></td>
			<td></td>
			<td>Homemade guillotine-like device for vitrification of EM grids</td>
		</tr>
		<tr>
			<td>Talos Arctica</td>
			<td>FEI/Thermo Fisher</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>UltrAufoil R1.2/1.3 300 mesh grids</td>
			<td>Quantifoil</td>
			<td>N1-A14nAu30-01</td>
			<td></td>
		</tr>
	</tbody>
</table>

single-particle cryo-em data collection with stage tilt using leginon

Single-particle analysis (SPA) by cryo-electron microscopy (cryo-EM) is now a mainstream technique for high-resolution structural biology. Structure determination by SPA relies upon obtaining multiple distinct views of a macromolecular object vitrified within a thin layer of ice. Ideally, a collection of uniformly distributed random projection orientations would amount to all possible views of the object, giving rise to reconstructions characterized by isotropic directional resolution. However, in reality, many samples suffer from preferentially oriented particles adhering to the air-water interface. This leads to non-uniform angular orientation distributions in the dataset and inhomogeneous Fourier-space sampling in the reconstruction, translating into maps characterized by anisotropic resolution. Tilting the specimen stage provides a generalizable solution to overcoming resolution anisotropy by virtue of improving the uniformity of orientation distributions, and thus the isotropy of Fourier space sampling. The present protocol describes a tilted-stage automated data collection strategy using Leginon, a software for automated image acquisition. The procedure is simple to implement, does not require any additional equipment or software, and is compatible with most standard transmission electron microscopes (TEMs) used for imaging biological macromolecules.

DPS at 0.3 mg/mL was used to demonstrate imaging at 0&#176;, 30&#176;, and 60&#176; tilts. Data from different tilt angles were collected on the same grid at different grid regions. CTF resolution fits for higher angle tilts tend to be poorer, as was the case when comparing the three datasets in this study. Figure 4 demonstrates comparative representative images and 2D classification averages. Although the protein concentration is unchanged across the different tilt angles, a higher tilt ang...

Watch this Scientific Journal Video about Single-Particle Cryo-EM Data Collection with Stage Tilt using Leginon at JoVE.com

Single-Particle Cryo-EM Data Collection with Stage Tilt using Leginon

The present protocol describes a generalized and easy-to-implement scheme for tilted single-particle data collection in cryo-EM experiments. Such a procedure is especially useful for obtaining a high-quality EM map for samples suffering from preferential orientation bias due to adherence to the air-water interface.

Single-particle analysis (SPA) by cryo-electron microscopy (cryo-EM) is now a mainstream technique for high-resolution structural biology. Structure ...

Tilting the specimen stage provides a simple and generalizable way of increasing the orientation distribution of particles during single-particle cryo-EM data collection. The uniform distribution of particles obtained due to specimen stage tilting enables the improvement of overall map quality and interpretability. Begin by aligning the microscope to ensure parallel illumination of the specimen and minimize coma aberrations.To identify the squares suitable for data collection, record a grid atlas without stage tilt or with stage tilt, which provides an overview of the overall grid quality and an initial indication of suitable areas for data collection. Inspect the squares manually at the magnification used in square acquisition node. Look for the squares where the foil is intact, does not look dehydrated, and has ideal ice thickness, and move the specimen stage to a square of interest.Determine the eucentric height for the stage position using an alpha wobbler at around 15 degrees stage tilt and adjust the Z height to bring the stage to eucentric height using the keypad panel for the microscope. Ensure the image shift is minimal during the alpha wobble routine. To find a more accurate Z height, estimate it in the focuser node at the magnification used in square acquisition node.Adjust the settings for the focuser node and enable or disable the fine Z focus option during the initial queuing of squares. Then press Simulate. Tilt the specimen stage to the desired tilt angle for data collection at the true eucentric height and recenter the stage if necessary.Press Simulate in the square acquisition node to begin queuing targets for whole acquisition node exposures. Next, select a Z focus target and regions with holes suitable for high magnification exposures and submit the targets to the queue for imaging. Bring the specimen stage back to its untilted state and then move to the next square.Repeat these steps until an adequate number of whole exposures have been queued. Once all squares are queued, go to the whole targeting node and press Submit Queued Targets. Select Allow for user verification of selected targets in node settings and manually inspect the targets selected by the high magnification exposure acquisition node to test if the automated EM hole finder can accurately identify the suitable regions for image acquisition when the specimen stage is tilted.Once the user is satisfied with the targeting accuracy, deselect the Allow for user verification of selected targets option for automated data collection. The representative images of the grid at square magnification with different tilt angles collected near and far from the eucentric Z height are shown here. The center of the beam is indicated by the center of the red concentric rings and the green arrow indicates the square of interest.There is a broken grid feature adjacent to the square of interest for reference. Shown here are the representative hole exposures and 2D class averages collected at 0 degrees, 30 degrees, and 60 degrees tilt angles. Although the protein concentration is unchanged across the different tilt angles, a higher tilt angle makes the imaged area appear more crowded in terms of particle concentration.2D class averages affected by overcrowding are shown in this red box. The simplicity of the protocol allows any standard user of the microscope to easily adapt a tilted data collection strategy.

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