Contents lists available at ScienceDirect Journal of Structural Biology journal homepage: www.elsevier.com/locate/yjsbi Technical Note Rapid increase of near atomic resolution virus capsid structures determined by cryo-electron microscopy Phuong T. Ho 1 , Vijay S. Reddy ⁎ Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA ARTICLE INFO Keywords: Cryo-electron microscopy Cryo-EM X-ray crystallography Virus structure Capsid structure ABSTRACT The recent technological advances in electron microscopes, detectors, as well as image processing and re- construction software have brought single particle cryo-electron microscopy (cryo-EM) into prominence for determining structures of bio-molecules at near atomic resolution. This has been particularly true for virus capsids, ribosomes, and other large assemblies, which have been the ideal specimens for structural studies by cryo-EM approaches. An analysis of time series metadata of virus structures on the methods of structure de- termination, resolution of the structures, and size of the virus particles revealed a rapid increase in the virus structures determined by cryo-EM at near atomic resolution since 2010. In addition, the data highlight the median resolution (∼3.0 Å) and size (∼310.0 Å in diameter) of the virus particles determined by X-ray crys- tallography while no such limits exist for cryo-EM structures, which have a median diameter of 508 Å. Notably, cryo-EM virus structures in the last four years have a median resolution of 3.9 Å. Taken together with minimal sample requirements, not needing diffraction quality crystals, and being able to achieve similar resolutions of the crystal structures makes cryo-EM the method of choice for current and future virus capsid structure determi- nations. 1. Introduction Although X-ray crystallography has been the method of choice for obtaining high resolution structural information for decades, cryo-EM has recently emerged as a good alternative for the structure determi- nation of bio-molecules (Kuhlbrandt, 2014; Nogales, 2016), especially in the case of large assemblies like viruses and ribosomes ever since the determination of the first near atomic resolution cryo-EM structures (Amunts et al., 2015; Bai et al., 2013; Chen et al., 2009; Jiang and Tang, 2017; Yu et al., 2008). The recent improvements in achieving higher resolutions of bio-molecular structures by single particle cryo-EM that has been branded as “resolution-revolution”, are made possible by a number of technological advances: 1) High-powered electron micro- scopes equipped with auto sample loaders (e.g., 300 kV Titan Krios (FEI)), 2) Superior direct electron detectors, such as the K2 Summit detector (Gatan Inc.), Falcon III (FEI) that improve upon the original Direct Electron detectors (Brilot et al., 2012) and are able to collect images as movies with short exposure times, 3) Software to collect (Glaeser et al., 2011; Suloway et al., 2005) and process the images (Grant and Grigorieff, 2015; Li et al., 2013; Zheng et al., 2017) as well as integrated pipelines to pick and classify particles (Lander et al., 2009; Tang et al., 2007) and perform subsequent image reconstructions (Ludtke et al., 1999; Lyumkis et al., 2013; Scheres, 2012; Yan et al., 2007), and 4) Requirement of only small amounts of samples without the need to produce diffraction quality crystals. To highlight the impact of the above technological advances on the structure determination of spherical viruses in particular, we have analyzed data on the methods of structure determination, the resolution of the structures, and the size (diameter) of the particles since the late 1970s when the first virus crystal structures were determined (Abad- Zapatero et al., 1980; Harrison et al., 1978) and deposited in RCSB-PDB (Berman et al., 2000). We obtained the relevant information from VI- PERdb (http://viperdb.scripps.edu), a repository and knowledge base of icosahedral virus structures (Carrillo-Tripp et al., 2009) represented in a single icosahedral convention and curated from the original entries deposited in RCSB-PDB. In addition to estimating the number of structures determined yearly by X-ray crystallography and cryo-EM, we have monitored the trends in improvements of resolution of the struc- tures achieved by both methods over the years as well as the size (diameter) of the virus particles. Consideration was also given to the Electron Microscopy Data Bank (EMDB) (http://www.emdatabank.org/ ), which has come to existence in the early 2000s as a repository of http://dx.doi.org/10.1016/j.jsb.2017.10.007 Received 30 July 2017; Received in revised form 28 September 2017; Accepted 18 October 2017 ⁎ Corresponding author. 1 Current address: Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. E-mail address: reddyv@scripps.edu (V.S. Reddy). Journal of Structural Biology xxx (xxxx) xxx–xxx 1047-8477/ © 2017 Elsevier Inc. All rights reserved. Please cite this article as: Ho, P.T., Journal of Structural Biology (2017), http://dx.doi.org/10.1016/j.jsb.2017.10.007