Routine single particle CryoEM sample and grid characterization by tomography
- New York Structural Biology Center, United States
- City College of New York, United States
- Columbia University, United States
- National Institutes of Health, United States
Abstract
Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1,000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation. We also show that fiducial-less cryo-electron tomography on single particle grids may be used to determine ice thickness, optimal single particle collection areas and strategies, particle heterogeneity, and de novo models for template picking and single particle alignment.
Data availability
Several representative tilt-series from the datasets have been deposited to the Electron Microscopy Data Bank (EMDB) in the form of binned by 4 or 8 tomograms and to the Electron Microscopy Pilot Image Archive (EMPIAR) in the form of unaligned tilt-series images (one including super-resolution frames), Appion-Protomo tilt-series alignment runs, and aligned tilt-series stacks.Protomo estimations for the orientation of the local ice normal based on the tilt-series alignment of the particles in the ice, which includes potential systematic stage and beam axis error, are available in all deposited EMPIAR datasets as a plot located: protomo_alignments/tiltseries####/media/angle_refinement/series####_orientation.gifA Docker-based version of Appion-Protomo fiducial-less tilt-series alignment is available at http://github.com/nysbc/appion-protomo.
Article and author information
Author details
Funding
Simons Foundation (SF349247)
- Clinton S Potter
- Bridget Carragher
National Institutes of Health (R01 GM084162)
- David Jeruzalmi
New York State Foundation for Science, Technology and Innovation
- Clinton S Potter
- Bridget Carragher
National Institute of General Medical Sciences (GM103310)
- Clinton S Potter
- Bridget Carragher
Agouron Institute (F00316)
- Clinton S Potter
- Bridget Carragher
National Institutes of Health (S10 OD019994-01)
- Clinton S Potter
- Bridget Carragher
National Institute on Minority Health and Health Disparities (5G12MD007603-30)
- David Jeruzalmi
National Institute of Allergy and Infectious Diseases (Intramural Funding from the Vaccine Research Center)
- Peter D Kwong
Agency for Science, Technology and Research
- Yong Zi Tan
National Institutes of Health (R01-MH1148175)
- Lawrence Shapiro
The authors declare that the funders played no role in this work, including the experimental design, data collection, or data analysis.
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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Routine single particle CryoEM sample and grid characterization by tomography
eLife 7:e34257.
https://doi.org/10.7554/eLife.34257
Further reading
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- Structural Biology and Molecular Biophysics
BTB (bric-a-brack, Tramtrack, and broad complex) is a diverse group of protein-protein interaction domains found within metazoan proteins. Transcription factors contain a dimerizing BTB subtype with a characteristic N-terminal extension. The Tramtrack group (TTK) is a distinct type of BTB domain, which can multimerize. Single-particle cryo-EM microscopy revealed that the TTK-type BTB domains assemble into a hexameric structure consisting of three canonical BTB dimers connected through a previously uncharacterized interface. We demonstrated that the TTK-type BTB domains are found only in Arthropods and have undergone lineage-specific expansion in modern insects. The Drosophila genome encodes 24 transcription factors with TTK-type BTB domains, whereas only four have non-TTK-type BTB domains. Yeast two-hybrid analysis revealed that the TTK-type BTB domains have an unusually broad potential for heteromeric associations presumably through a dimer-dimer interaction interface. Thus, the TTK-type BTB domains are a structurally and functionally distinct group of protein domains specific to Arthropodan transcription factors.
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- Structural Biology and Molecular Biophysics
In eukaryotes, RNAs transcribed by RNA Pol II are modified at the 5′ end with a 7-methylguanosine (m7G) cap, which is recognized by the nuclear cap binding complex (CBC). The CBC plays multiple important roles in mRNA metabolism, including transcription, splicing, polyadenylation, and export. It promotes mRNA export through direct interaction with a key mRNA export factor, ALYREF, which in turn links the TRanscription and EXport (TREX) complex to the 5′ end of mRNA. However, the molecular mechanism for CBC-mediated recruitment of the mRNA export machinery is not well understood. Here, we present the first structure of the CBC in complex with an mRNA export factor, ALYREF. The cryo-EM structure of CBC-ALYREF reveals that the RRM domain of ALYREF makes direct contact with both the NCBP1 and NCBP2 subunits of the CBC. Comparing CBC-ALYREF with other cellular complexes containing CBC and/or ALYREF components provides insights into the coordinated events during mRNA transcription, splicing, and export.
