Research Article

Atomic structure of the human cytomegalovirus capsid with its securing tegument layer of pp150

See allHide authors and affiliations

Science  30 Jun 2017:
Vol. 356, Issue 6345, eaam6892
DOI: 10.1126/science.aam6892
  • A 3.9-Å structure of human cytomegalovirus.

    One of the 60 asymmetric units that make up HCMV’s 1320-Å-wide capsid is rendered above a colored face of the icosahedral shell. Atomic models of the capsid proteins (SCP, MCP, Tri1, Tri2A, and Tri2B) and capsid-associated pp150 tegument protein (“nt” signifies the N-terminal one-third) reveal a suite of strategies that work in a synergistic manner to stabilize a capsid that is highly pressurized by HCMV’s enormous 235-kb genome. P, peripentonal; C, center; E, edge; Ta to Te, heterotrimeric triplexes composed of Tri1, Tri2A, and Tri2B.

  • Fig. 1 CryoEM reconstruction and atomic modeling of HCMV.

    (A) Central slices of HCMV virion (top) and noninfectious enveloped particle (NIEP, bottom) reconstructions at 15 Å. The inset shows a 23-Å dsDNA interlayer distance and dsDNA density within hexon channels. (B) Radially colored HCMV reconstruction at 3.9-Å resolution viewed along a twofold axis. Fivefold, threefold, and twofold axes are denoted by a pentagon, triangle, and oval, respectively. P (peripentonal), C (center), and E (edge) denote hexons and Ta to Tf denote triplexes that together contribute to an asymmetric unit. (C) Density map (mesh) and atomic model of an MCP helix illustrate side chain features. A, alanine; E, glutamic acid; F, phenylalanine; H, histidine; L, leucine; N, asparagine; Q, glutamine; R, arginine; a.a., amino acids. (D) Asymmetric unit colored by protein subunit type. MCPs (gray) make up pentons and hexons. Triplexes are heterotrimers composed of Tri1 (blue) and a Tri2A (cyan)–Tri2B (magenta) dimer. SCPs (bright green) bind to all MCPs, whereas pp150 tegument proteins (red) cluster above triplexes. Rainbow ribbon models show individual proteins and conformers (blue N terminus through green and yellow to red C terminus). pp150nt, N-terminal one-third of pp150.

  • Fig. 2 MCP organization and structure.

    (A) Canonical hexon MCP colored and labeled by domain. N- and C-termini in ribbon models are henceforth marked with blue and red circles, respectively. (B) MCP floor region (purple) superposed with HK97 gp5 (light blue) illustrates common usage of the Johnson fold. The inset shows the MCP Johnson fold domain’s β-core, colored as in (C). (C) Schematic of MCP organization relative to a canonical Johnson fold. Black bars indicate HCMV MCP domain insertion sites. Johnson fold N-, α-, and β-elements (33) are colored cyan, green, and magenta, respectively. The E-loop and P-subdomain are contained within the N- and β-elements, respectively. H’s indicate helices. (D) Pipe-and-plank depictions of adjacent hexon MCP towers show extensive interactions at a helix-loop interface (magenta box). Superposing HSV-1 VP5 upper domain (VP5ud, green) and HCMV MCP upper domain (MCPud, purple) reveals similarities in secondary and tertiary structure, with differences pronounced at the upper SCP-binding loop regions (insets). Other colors are as in (C).

  • Fig. 3 Features of the hexon channel.

    (A) β-sheet augmentations between neighboring channel domains result in six β-strands from one MCP channel domain interacting with β22 from an adjacent channel domain to form a seven-stranded β-sheet. (B) Six seven-stranded β-sheets form a daisy chain–like β-sheet ring (inset) around the hexon channel, connected by six constricting loops that define the narrowest region of the channel. (C) Electrostatic surface rendering of a clipped hexon channel. Blue and red denote positive and negative charge, respectively. (D) Top view of (C), showing that upper channel regions are predominantly negatively charged. (E) Bottom view of (C), showing that DNA-accommodating lower channel regions are predominantly positively charged.

  • Fig. 4 Three classes of capsid floor–defining interactions.

    (A) Overview of MCPs from C, E, and P hexons. Local threefold (triangle) and twofold (oval) axes are indicated. The inset shows the three major types of MCP-MCP interactions (boxed), subsequently illustrated in detail. (B) Intracapsomer interactions (type I) occur between adjacent MCPs within a capsomer and consist of two sets of floor region β-sheet augmentations (inset). (C) Dimerization interactions (type II) are intercapsomer interactions that occur between MCP dimerization domains across a local twofold axis. Insets show quasi-equivalent helix interactions between two dimerization domains. (D) N-lasso (type III) interactions are facilitated by an MCP N-lasso (green) that extends and lashes around the E-loop (orange) and N-lasso neck (blue) of two MCPs located diagonally across a local twofold axis (upper inset). Three pairs of N-lasso interactions form an enclosed lasso triangle around the local threefold axis. E1’s N-lasso also augments the existing β-sheet from C5 and C4’s type I interaction to form a seven-stranded β-sheet complex (lower inset). Helices from C5’s helix-hairpin (H6 and H7) and buttress (H49) domains form a helix bundle with E1 N-lasso’s H2, further securing E1’s N-lasso.

  • Fig. 5 MCP adaptations at the fivefold axis.

    (A) Superposing hexon MCP (teal) and penton MCP (burgundy) reveals a contracted and rotated penton MCP floor region relative to hexon MCP. (B) Superposing hexons and pentons reveals that pentons have a more “closed umbrella” shape relative to hexons. (C) Superposed canonical hexon MCP, penton MCP, P1, and P6 reveal similar floor regions with differences at the N-lasso and dimerization domains. Penton MCP and P6 adopt an “open” N-lasso conformation (magenta inset), whereas penton MCP and P1 adopt distinctive extended conformations of the dimerization domain (green inset). (D) Overview of penton, P1, P2, and P6 MCPs. The inset demonstrates how, because of local geometry changes near the fivefold axis, penton MCPs participate in neither N-lasso lashing nor dimerization interactions with surrounding hexon MCPs. (E) Comparison of buttress supports of hexon and penton MCP buttress domains. A hexon buttress support, akin to a flexed elbow, contains two helices that support the MCP tower and clamps a neighboring MCP’s N-lasso (left). Penton MCPs are not lashed by P6’s open N-lasso; a penton buttress support extends its elbow to form a long helix reaching to the MCP floor, where it contributes β37 to the floor’s E-loop β-sheet complex while supporting the penton tower (right).

  • Fig. 6 Triplex structure and interactions with MCP.

    (A) Overview of Tb triplex and its surrounding MCPs. Insets show MCP buttress arms that clamp the upper junction regions of the triplex proteins. (B) Tri2A and Tri2B form dimers that interact closely with the capsid floor. Their bottom views reveal similar clamp and trunk domain footprints, albeit rotated 120° about each other. (C) Pipe-and-plank depictions of Tri2 dimer in profile and top views, illustrating the helix bundle formed from the embracing arm domains of Tri2A and Tri2B. (D) Superposing Tri2A and Tri2B reveals nearly identical clamp and trunk domains but highlights conformational differences in their embracing arms. (E) Tri1’s main mass exhibits little contact with the capsid floor compared with Tri2 dimer. Instead, Tri1 secures Tri2 dimer to the capsid through a latch-and-anchor function. Tri1’s third-wheel domain wedges into Tri2’s embracing arms, latching Tri1 to Tri2 dimer (green perspective; the pipe-and-plank depiction shows this at a rotation of 90°). Meanwhile, Tri1’s N-anchor penetrates the capsid floor to anchor the complete triplex to the capsid shell (red and blue perspectives).

  • Fig. 7 SCP and securing tegumental pp150 to the capsid.

    (A) SCPs (bright green) ring the outer circumference of both hexon and penton capsomers. (B) SCP interacts with the underlying MCPud primarily through SCP’s C-terminal helix and loop (left). Electrostatic potential surfaces of SCP (center and right), SCP-bound MCPud (center), and MCPud (right) reveal a shallow cleft atop MCPud (green box) into which SCP inserts. (C) Three pp150 conformers—pp150nt-a (red), pp150nt-b (orange), and pp150nt-c (purple)—cluster on each triplex and extend toward the SCPs atop nearby MCPs, shown here at Tb triplex. (D) Ribbon model of pp150nt, showing that it is organized into upper and lower helix bundles. Green residues denote β-herpesvirus–conserved regions CR1 and CR2, and yellow residues denote the primate CMV–conserved cysteine tetrad (cys). (E to G) Profile views of the interactions of pp150nt-a, -b, and -c with capsid proteins, respectively. Interactions between pp150nt-a’s upper end and the capsid occur through a cysteine tetrad–to-SCP interaction [(E), right insets], which is maintained in all conformers. Interactions between pp150nt’s lower end and the capsid vary among conformers. pp150nt-a’s lower end interacts with a neighboring MCP’s tower [(E), top left inset] and underlying Tri2A and Tri2B [(E), bottom left inset], whereas the lower ends of pp150nt-b and pp150nt-c interact exclusively with Tri1 and Tri2B [(F), inset] and Tri2A and Tri2B [(G), inset], respectively.

  • Fig. 8 Hexon and penton stabilization by pp150nt.

    (A) Top view of a P hexon and its interacting SCP and pp150nt molecules, showing that a P hexon is stabilized by eight copies of pp150nt. (B) Side view of (A). (C) Top view of a penton and its interacting SCP and pp150nt molecules, showing that a penton is stabilized by 10 copies of pp150nt. In addition to the five pp150nt molecules associated with each penton SCP, five pp150nt-c molecules from five surrounding P6 SCPs also interact with each penton MCP. These peripentonal pp150nt-c conformers represent a special case normally seen only with pp150nt-a, where the lower helix bundle interacts directly with an MCP tower in addition to an underlying triplex. (D) Side view of (B).

  • Movie 1 The HCMV capsid at 3.9 Å

    A fly-in perspective of the radially colored HCMV reconstruction density map.

  • Movie 2 HCMV major capsid protein.

    Atomic model of the major capsid protein colored by domain. The rainbow color scheme that initially appears progresses from the N terminus (blue) to the C terminus (red).

  • Movie 3 HCMV triplex proteins.

    An overview of Tri1, Tri2A, and Tri2B, including a comparison of Tri2A and Tri2B, and an illustration of how the heterotrimeric triplex is composed from its constituent proteins. The rainbow color scheme that appears temporarily for each protein progresses from the N terminus (blue) to the C terminus (red).

  • Movie 4 Interactions of the HCMV lock unit.

    An overview of the three classes of MCP-MCP interactions that characterize the capsid floor and the role of the triplex in securing the capsid floor. Purple, yellow, red, orange, pink, and green indicate hexon MCPs. Blue, cyan, and magenta indicate triplex proteins.

  • Movie 5 Interactions of HCMV tegument protein pp150 and capsid.

    An overview of pp150nt’s upper- and lower-end interactions with capsomer protrusions and the underlying triplex, respectively. Variations in pp150nt lower-end interactions with the underlying triplex are shown for different pp150nt conformers.

  • Atomic structure of the human cytomegalovirus capsid with its securing tegument layer of pp150

    Xuekui Yu, Jonathan Jih, Jiansen Jiang, Z. Hong Zhou

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

    Download Supplement
    • Figs. S1 to S10
    • References

Navigate This Article