The amazing HK97 fold: versatile results of modest differences

Abstract

dsDNA Bacteriophages, some dsDNA archaeal viruses and the Herpesviruses share many features including a common capsid assembly pathway and coat protein fold. The coat proteins of these viruses, which have the HK97 fold, co-assemble with a free or attached scaffolding protein and other capsid proteins into a precursor capsid, known as a procapsid or prohead. The procapsid is a metastable state that increases in stability as a result of morphological changes that occur during the dsDNA packaging reaction. We review evidence from several systems indicating that proper contacts acquired in the assembly of the procapsid are critical to forming the correct morphology in the mature capsid.

Figure 1.. Components and features of capsids.

A. The HK97 fold with important common features labeled and color-coded as indicated in the figure. The ribbon diagram is from the mature HK97 capsid chain A (PDB 1OHG). B. The size range of the HK97 fold. Shown are images of surface rendered cryo-EM density maps from the T=1 encapsulin of Thermotoga maritima [6], the P22 mature capsid [19], and Bacillus megaterium jumbophage G [7]. C. A hexon from the HK97 mature capsid colored as in (A). D. A generic pathway for capsid assembly that applies, in general features, to nearly all double-stranded DNA tailed phages and Herpesviruses. *Note that while a capsid maturation protease is a common feature, there are many bacteriophages that do not utilize one. E. Examples of the shape changes of capsomers that occur when procapsids convert to mature procapsids. Surface rendered images are shown of the hexons and pentons of phage HK97 from X-ray structures (PDB ID 3E8K (procapsid) and 1OGH (mature)). Structural models in figures were visualized using Chimera [47] or SPDBV [48].

Figure 2.. HK97 fold gallery.

Nine examples of the HK97 fold determined by X-ray crystallography or cryo-electron microscopy with secondary structure colored from N- to C-termini in blue to red hues. Protruding G-loops are colored orange, I-domains (Insertion domains) are colored magenta. Panels, in order: a, phage HK97 mature capsid protein [43]; b, Thermotoga maritima encapsulin [6]; c, Pyrococcus furiosus encapsulin (previously “PFV” for Pyrococcus fuiosus virus-like particle [39]); d, phage T4 mature major capsid protein gp23* [49]; e, P22 coat protein [19]; f, epsilon 15 mature capsid protein [50]; g, 80alpha procapsid major capsid protein [42]; h, phage TW1 major capsid protein [18]; i, phage T7 major capsid protein from the procapsid [41].

Figure 3.. Procapsid gallery.

Ten examples of procapsid structures from the Protein Data Base (PDB) or Electron microscopy database (EMDB) rendered at low resolution using Chimera [47] so that the shapes of the procapsid hexons can be discerned. Procapsids are round (not angular) and have lumpy capsomers with a domed and asymmetric shape, as noted in the text. The procapsids are radially cued with yellow being the furthest from and blue being closest to the center of each particle. The scale bar represents 20 nm. Shown are the procapsids of phages HK97 (PDB 3E8K, [17]); T7 (EMD-1321 ,[51]); Gifsy-2 (EMD-1691, [52]); Lambda (EMD-1507, [53]); 80alpha (EMD-7030, PDB 6B0X;[42]); P2 (EMD-5406, [54]); P22 (EMD-5149, [15]); Sf6 (EMD-5724, [55]); SIO2 (EMD-5383, [56]); and T5 (not deposited, [57]).

Figure 4.. Capsid protein interactions that are important for assembly.

Inter and intra-capsomer interactions discussed in the text are illustrated in close-up views. A. The site of inter-capsomer interactions between phage P22 coat protein D-loops. This shows the interaction in the mature capsid [19], but similar interactions occur in procapsids during assembly [22,38,58]. B. Interactions between the E-loops (in red) and G-loops (in orange) of adjacent capsomers in HK97 procapsids (PDB ID 3e8k). These interactions (mediated by residues K178 (in cyan) on the E-loop and D231 (orange) on the G-loop) have been shown to be important for controlling the assembly of procapsids, but are not present in the mature capsid [13]. C. Interactions made by HK97 E-loops (shown as red ribbons) within capsomers. Residue E153 (in red) on the E-loop interacts with R210 (in blue) on the backbone helix of the adjacent subunit. These interactions are essential for assembly of the HK97 major capsid protein into procapsids [12]. The figure shows the mature capsid (PDB ID 1OHG), but the interactions are present at all stages of HK97 assembly.