P68 Phage density obtained by Cryo-Electron Microscopy

<p>We clarify that this density map was created by Dominik Hrebik. However it is to be included in a larger manuscript, with other authors, currently under review at Nucleic Acids Research. The title, author list, and abstract of that manuscript follow:</p><h2>Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses&nbsp;</h2><p>Samuel Coulbourn Flores1,&nbsp;Michal Malý2, Dominik Hrebík3,<strong>&nbsp;</strong>Pavel Plevka3,&nbsp;Jiří Černý2</p><p>1Swedish University of Agricultural Sciences, Ulls Väg 26, Uppsala, and Stockholm University, Tomtebodavägen 23A, Solna, Sweden</p><p>2&nbsp;Institute of Biotechnology of the&nbsp;Czech Academy of Sciences, Prumyslova 595, Vestec, 25250, Czech Republic</p><p>3Central European Institute of Technology,&nbsp;Kamenice 753/5, Brno, Czech Republic</p><h2>Abstract</h2><p>The revolution in Cryo-Electron Microscopy has resulted in unprecedented power to resolve large macromolecular complexes including viruses. Many methods exist to explain density corresponding to proteins and thus entire protein capsids have been solved at the all-atom level.&nbsp;However methods for nucleic acids lag behind, and no all-atom viral double-stranded DNA&nbsp;genomes have been published at all. We here present a method which exploits the spiral&nbsp;winding patterns of DNA in icosahedral capsids. The method quickly generates shells of DNA wound in user-specified, idealized spherical or cylindrical spirals. For transition regions, the method allows guided semiflexible fitting. For the <i>kuravirus&nbsp;</i>SU10, our method explains most of the density in a semiautomated fashion.&nbsp;The results suggest rules for DNA turns in the end caps under which two discrete parameters determine the capsid inner diameter. We suggest that other kuraviruses viruses may follow the same winding scheme, producing a discrete rather than continuous spectrum of capsid inner diameters. Our software may be used to explain the published density maps of other double-stranded DNA viruses and uncover their genome packaging principles.</p><p>&nbsp;</p>