Fig. 4: DNA forms split ring encircling portal complex of phage 812 genome release intermediate.
From: Genome anchoring, retention, and release by neck proteins of Staphylococcus phage 812
A, B Surface representation of an asymmetric cryo-EM reconstruction of the neck of phage 812 genome release intermediate (EMD-18395), low-pass filtered to 6 Å and zone-colored based on its structural components: dsDNA in red, portal proteins in light blue, adaptor proteins in gold; remaining density in semi-transparent gray. The arc distance between neighboring portal wing domains described by the anchor DNA is 34 Å (indicated in navy blue), which corresponds to one B-DNA helix turn. C–E Interactions between side chains of portal proteins and DNA in C12-symmetrized reconstruction of the neck of the genome release intermediate (EMD-18213). The two DNA strands are colored in primary red (strand F) and rose red (strand R). Turquoise asterisks denote the bases forming putative hydrogen bonds with the Lys138 side chain. F Plot of the average van der Waals width of the minor groove over one helical turn of the DNA anchored to the portal complex (n = 12 helical turns). G Mapping of sequence reads of DNA remaining in phage 812 capsids after genome release onto phage 812 long terminal repeat (LTR). H Shape of the DNA minor groove facing the portal protein binding site.
