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JOURNAL OF STRUCTURAL BIOLOGY 124, 70–76 (1998)

ARTICLE NO. SB984055

Structure of the Human Cytomegalovirus B Capsid by Electron


Cryomicroscopy and Image Reconstruction
S. J. Butcher,*,1 J. Aitken,† J. Mitchell,* B. Gowen,‡ and D. J. Dargan*
*MRC Virology Unit and †Institute of Biomedical and Life Sciences, Division of Virology, University of Glasgow, Church Street,
Glasgow G11 5JR, United Kingdom; and ‡Department of Biochemistry, Imperial College of Science, Technology, and Medicine,
London SW7 2AZ, United Kingdom
Received June 22, 1998, and in revised form October 23, 1998

kinetics, and ability to spread in culture) and genetic


The three-dimensional structure of B capsids of relatedness. Herpesviruses genomes vary consider-
the b-herpesvirus human cytomegalovirus (HCMV) ably in size (125–245 kb), G 1 C content (32–75%),
was investigated at a resolution of 3.5 nm from and sequence organization, but these characteristics
electron cryomicrographs by image processing and
are independent of subfamily classification (Roiz-
compared with the structure obtained for the a-her-
man et al., 1992). DNA sequence and genetic analy-
pesvirus herpes simplex virus type 1 (HSV-1). The
main architectural features of the HSV-1 and HCMV sis of viruses from each subfamily have revealed a
capsids are similar: the T 5 16 icosahedral lattice set of common ‘‘core’’ genes that are conserved in the
consists of 162 capsomers, composed of two distinct viral DNA sequence. Core genes provide common
morphological units, 12 pentamers and 150 hexa- functions and encode proteins required for viral DNA
mers, with triplex structures linking adjacent cap- metabolism, DNA replication, and assembly of the
somers at positions of local threefold symmetry. The viral capsid structure and some virus envelope glyco-
main differences in the HSV-1 and HCMV capsids proteins with a role in virus entry (Davison, 1993).
are found in the diameter of the capsids (125 and 130 Other genes appear to be specifically conserved only
nm, respectively); the hexamer spacing and relative within subfamilies and must have a role in confer-
tilt (center-to-center hexon spacing at outer edge, ring subfamily biological characteristics.
17.9 and 15.8 nm, respectively); the morphology of Herpesviruses share a common virion architec-
the tips of the hexons (similar in length but 33% ture. The double-stranded DNA genome is contained
thinner in HCMV); and the average diameter of the
within an icosahedrally symmetric capsid, though it
scaffold (44 and 76 nm, respectively). By analogy
is not yet clear how this large DNA molecule folds
with HSV-1, the mass on the HCMV hexon tip is
attributed to the smallest capsid protein (HCMV
itself into the liquid crystalline packaged form (Booy
gene UL48/49). The differences in capsid structure et al., 1991). However, there is no convincing evi-
are discussed in relation to the ability of the HCMV dence that the DNA is spooled around a protein core
structure to package a genome some 60% larger than in the shape of a torus as earlier reported (Furlong et
that of HSV-1. r 1998 Academic Press al., 1972). The nucleocapsid is surrounded by a
Key Words: human cytomegalovirus; three-dimen- complex protein layer known as the tegument and
sional structure; electron cryomicroscopy. enveloped by a lipid-rich membrane decorated with
virus glycoprotein spikes.
The capsid shell architecture of the a-herpesvi-
INTRODUCTION
ruses herpes simplex virus type 1 (HSV-1) (Booy et
Herpesviridae is a family of large and complex al., 1988; Schrag et al., 1989; Zhou et al., 1994),
viruses ubiquitous in nature and infecting diverse equine herpesvirus type 1 (EHV-1) (Baker et al.,
animal species. The family is classified into a-, b-, 1989), and the more distantly related channel catfish
and g-herpesvirus subfamilies on the basis of shared virus (CCV) (Booy et al., 1996) has been studied by
biological properties (i.e., host range, replication cryomicroscopy and image reconstruction. The cap-
sid is organized on a T 5 16 lattice with 150
hexamers (hexons) and 12 pentamers (pentons).
1 Current address: Institute of Biotechnology and Department Intercapsomeric linkage is facilitated by triplex com-
of Biosciences, Division of Genetics, Biocenter 2, FIN-00014 plexes. The HSV-1 capsid shell proteins have been
University of Helsinki, Finland. localized by image reconstruction combined with

1047-8477/98 $25.00 70
Copyright r 1998 by Academic Press
All rights of reproduction in any form reserved.
STRUCTURE OF HUMAN CYTOMEGALOVIRUS 71

TABLE I
Location of the Four Major Components of the HSV Capsid Shell and Comparison to the HCMV Homologues
(Gibson, 1996)
HSV-1 HCMV
Copy
Location in capsid number Gene Gene product Gene Gene product

Hexons and pentons 960 UL19 VP5 (149 kDa) UL86 Major capsid protein (154 kDa)
Triplexes 640 UL18 VP23 (34 kDa) UL85 Minor capsid protein (35 kDa)
Triplexes 320 UL38 VP19c (50 kDa) UL46 Minor capsid protein-binding protein (33 kDa)
Hexon tips 900 UL35 VP26 (12 kDa) UL48/49 Smallest capsid protein (8.5 kDa)

difference imaging (Trus et al., 1995; Zhou et al., only limited amino acid homology, but both are small
1988b, 1995) and antibody labeling (Trus et al., 1992) proteins with a basic pI (Baldick and Shenk, 1996;
and are shown in Table I. Herpesvirus capsid assem- Gibson et al., 1996b).
bly and viral DNA packaging takes place in the We report differences between the HCMV and
nucleus of infected cells and is dependent on the HSV-1 capsid shell structures that are relevant to
virus scaffolding proteins [e.g., the product of HSV-1 the observation that the HCMV capsid structure
genes UL26 and UL26.5: and HCMV genes UL80 accommodates a DNA molecule up to 60% larger (at
and UL80.5 (Desai et al., 1994; Preston et al., 1992; 245 kb) (Cha et al., 1996; Chee et al., 1990; Dargan et
Tatman et al., 1994; Welch et al., 1991a,b)]. Three al., 1997) than that of the HSV-1 genome (152 kb)
types of capsid structure are generated: A, which are (McGeoch et al., 1988).
devoid of any core structure; B, which contain a
scaffold structure but lack viral DNA; and C, which MATERIALS AND METHODS
are mature DNA-containing structures (Gibson and
Cells
Roizman, 1972). The B-capsid structures are the
most abundant in the infected cell nucleus and most Human fetal foreskin fibroblast cells (HFFF-2; European Collec-
easily isolated. tion of Animal Cell Cultures, No. 86031405) were propagated in
Dulbecco’s modified Eagle’s medium containing 10% fetal bovine
This paper extends the investigation of capsid serum (DMEM 10% FB).
shell architecture to the b-herpesvirus subfamily.
Using electron cryomicroscopy and image reconstruc- Virus Propagation
tion, we have examined and compared the B-capsid The AD169 (Glasgow) stock of HCMV (Dargan et al., 1997) was
shell structures of two important human pathogens: used throughout. Virus-infected cell preparations were produced
human cytomegalovirus (HCMV), the prototype vi- by infecting HFFF-2 cell monolayers (4 3 106 cells) with HCMV at
rus of the b-herpesvirus subfamily, and HSV-1, the a multiplicity of infection of 0.01 PFU/cell and, when extensive
prototype virus of the a-herpesvirus subfamily. The cytopathic effect was evident, seeding virus-infected cells (,105
cells) onto subconfluent monolayers of HFFF-2 cells in roller
HCMV capsid shell proteins are compared with bottles (,2 3 107 cells/bottle) and incubating at 37°C. At 24 h
those of HSV-1 in Table I. The HSV-1 and HCMV postinfection (PI) the culture medium was replaced with fresh
major capsid proteins (MCPs) are of similar molecu- DMEM 10% FB and the infected cultures were incubated again at
lar size and their respective genes share 25% nucleo- 37°C. Cytopathic effect was usually apparent by the fifth day PI
tide and 26% amino acid homology (Chee et al., and was extensive by the ninth day. The infected cells were
detached from the surface of the roller bottle by gentle shaking
1989). The HSV-1 triplex structures are composed of and then pelleted by centrifugation at 1000g.
two proteins, VP23 (gene UL18) and VP19c (gene
UL38), in the ratio of 2:1. Similarly, the HCMV Capsid Preparation
triplex structures are composed of the minor capsid
Nuclei were isolated from the infected cell pellets by washing
protein-binding protein (mC-BP, gene UL46) and the the cells with NTE buffer (0.5 M NaCl, 20 mM Tris, pH 7.4, 1 mM
minor capsid protein (mCP, gene UL85), also in the EDTA) containing 1% Nonidet P-40. (NP40). The resulting nuclei
ratio of 2:1. However, while the HCMV mCP shares were pooled and stored at 270°C until required. The nuclei were
22.5% amino acid homology with HSV-1 UL18, the resuspended in NTE containing 1% NP40 and subjected to three
cycles of freeze–thawing. This suspension was then probe soni-
HCMV mC-BP protein is only two-thirds of the size cated to break residual nuclei open and the cellular debris
of its HSV-1 functional homologue and shares no pelleted at 1000g. The virus particles present in the supernatant
appreciable amino acid homology (Gibson et al., were pelleted through a 40% (w/v in NTE) sucrose cushion
1996a). The small HSV-1 protein, VP26, located at (Sorvall TST41, 25 000 rpm, 1 h, 4°C), resuspended in 1% NP40 in
the tip of the hexons is not required for capsid shell NTE, and banded on a 10–40% sucrose gradient in NTE (Sorvall
TST41, 40 000 rpm, 20 min, 4°C). The B-capsid band was har-
assembly (Tatman et al., 1994). HSV-1 VP26 and its vested, pelleted (Sorvall TST41, 25 000 rpm, 1 h, 4°C), and
HCMV counterpart, the ‘‘smallest capsid protein’’ resuspended in 0.15 M NaCl, 20 mM Tris, pH 7.4, 1 mM EDTA.
(SCP, reported as gene UL48.5, or UL48/49), have HSV capsids were purified from baby hamster kidney cells
72 BUTCHER ET AL.

infected for 16 h at 37°C with 5 PFU HSV-1 (strain 17) per cell, as
described previously (Zhou et al., 1994).

Electron Cryomicroscopy
Electron cryomicroscopy allows us to examine samples under
native, hydrated conditions free from some of the artifacts that
are commonly associated with negatively stained specimens, as
well as reveal internal details. Freshly prepared capsids were
vitrified on holey carbon coated grids by plunge freezing into
liquid ethane (Adrian et al., 1984; Fukami and Adachi, 1965).
Samples were held at less than 2170°C in an Oxford CT3500
cryostage and observed using low-dose techniques in a Jeol
JEM-1200 EX II electron microscope (120 kV, tungsten filament)
fitted with an Oxford TAC100 twin-blade anticontaminator. Focal
pairs were recorded on Kodak SO163 film using a dose of 10–15
e/Å2 at a nominal magnification of 25 000 or 30 000 at defocus
values between 3 and 4 µm. FIG. 1. Electron cryomicrograph of B capsids from HCMV.

Image Processing than those for HSV1 (see Results). The data from the Jeol
Selected micrographs were scanned on a Zeiss-SCAI scanner micrographs were then scaled accordingly. In addition the scaling
using a step size of 14 µm per pixel, corresponding to 0.58 nm per of the HSV-1 reconstruction was checked against that of a 1.9-nm
pixel (14/24 100) and 0.48 nm per pixel (14/29 000) on the speci- HSV-1 reconstruction kindly provided by Dr. Hong Zhou (Zhou et
men. Image quality was assessed and the defocus estimated by al., 1995).
evaluating the position of the first zero in the sum of power
spectra from the particles of each micrograph. In total six RESULTS
micrographs were scanned from which 144 particles were se-
lected, boxed, floated, and normalized using SPIDER (Frank et al., Electron Cryomicroscopy and Image Reconstruction
1981). Orientations and centers were determined and refined
We have studied the structure of the HCMV capsid
using the common lines procedure (Crowther, 1971; Fuller et al.,
1996). The polar Fourier transform method was used to check the by electron cryomicroscopy and image processing.
accuracy of the model, further refinement, and orientation searches Figure 1 shows part of an electron micrograph of
for new data (Baker and Cheng, 1996). Three-dimensional recon- vitrified HCMV B capsids. The capsids have a diam-
structions were calculated using cylindrical expansion methods eter of approximately 130 nm. This can also be seen
(Crowther, 1971). Only particles with icosahedral phase residuals
below 75° at 3.5-nm resolution were included in the reconstructions.
from the radial density profile (Fig. 2). The capso-
The map of HCMV was calculated to 3.5-nm resolution from a meres covering the surface of each capsid are clearly
subset of 59 particles from four micrographs (taken at 3 µm under evident as projections at the edge of the particle and
focus). All the eigenvalues were greater than 10 and 97% were as regularly spaced dots across the surface (,15 nm
greater than 100, showing that reciprocal space was adequately in diameter). In addition the scaffold can be seen as a
sampled. Independent reconstructions calculated from subsets of
the data were consistent with all the features described below. For
dense area, roughly in the center of each particle.
comparison, a micrograph of HSV-1 B capsids (taken at 3 µm The HCMV capsids were difficult to fully dissoci-
under focus) was also processed in a similar fashion. Here, 38 of 43 ate from the nuclear matrix without breakage, and
particles were included in the reconstruction that was also could not be stored at 270, 220, or 4°C without
calculated to 3.5-nm resolution. For this reconstruction, all of the further breakage occurring. Consequently, only rela-
eigenvalues were greater than 1 and 87% were greater than 100,
reflecting the lower number of particles included in the reconstruc- tively few particles from each field could be used
tion. Visualization and rendering of the reconstructions were done (typically 30 particles were processed per micro-
in SPIDER. All of the programs were run on a Digital Alpha 255/233
AXP running Digital Unix OSF1 v3.2, an SGI Indigo Elan 4000
running IRIX 5.2, and a Digital Alpha 2100 running Open VMS 7.0.
To address the scaling of the micrographs, additional data were
collected on a CM200 FEG microscope at 200 kV, using prepara-
tions mixed with tomato bushy stunt virus [TBSV, 38.5 nm in
diameter in the presence of 1 mM EDTA, pH 7.4 (Robinson and
Harrison, 1982)] to act as an internal standard. These data (taken
at defocus values of 5605 and 6120 nm for HSV-1 and 5200, 5605,
and 5610 nm for HCMV, at a magnification of 319 400, and
scanned with a 7-µm step size) could be corrected for the micro-
scope contrast transfer function due to the presence of several
minima in the power spectra, unlike the original data collected on
the Jeol 1200EX with a tungsten filament. For each micrograph,
at least 90 TBSV particles were aligned and a radial profile made
of the average to check the magnification. The HSV1 data (134
particles) and the HCMV data (70 particles) were averaged FIG. 2. Graph showing the radial density distribution of B
separately and gave rise to radial profiles similar to those shown capsids from HCMV (solid line) and HSV-1 (broken line) calcu-
in Fig. 2, where the shell peaks for HCMV are at a larger radius lated from the reconstructions shown in Fig. 3.
STRUCTURE OF HUMAN CYTOMEGALOVIRUS 73

FIG. 3. Comparison of HCMV and HSV-1 reconstructions. Surface representations of HCMV (A) and HSV-1 (B) viewed down an
icosahedral twofold axis of symmetry contoured at one standard deviation above the mean density value. The inset shows the positions of
hexamers (white dots) and pentamers (green dots) within 1 facet of a T 5 16 lattice, in an orientation similar to that of the reconstructions.
Central 0.58-nm-thick sections through the HCMV (C) and the HSV-1 (D) reconstructions. Bar 5 50 nm.

graph), so data from several micrographs were com- organized on a T 5 16 icosahedral lattice (Fig. 3A).
bined to yield the final reconstruction. There was The relative positions of the capsomers (hexamers
also a high rejection rate during the common lines and pentamers) within a facet are shown in the top
refinement as up to 60% of the particles per micro- inset of Fig. 3.
graph gave icosahedral phase residuals greater than
75°, even at 3.5-nm resolution, and were therefore Capsomers
excluded from the reconstruction. The HCMV hexons and pentons form cylindrical
protrusions (Figs. 3A, 3C, 4) penetrated by an axial
Three-Dimensional Structure channel constricted 7.4 nm from the base of the
The major structural components of the HCMV B capsomer. The hexons appear slightly skewed, so
capsid are 150 hexons, 12 pentons, and 320 triplexes that the axial channel is oval rather than round. The
74 BUTCHER ET AL.

Comparison with HSV-1 B Capsids


The basic elements of the HSV-1 reconstruction
described here are similar to those reported by
others (Booy et al., 1994; Newcomb et al., 1993; Trus
et al., 1992, 1995; Zhou et al., 1998a, 1995) although
the structure was calculated independently.
The HCMV B capsid has a diameter larger than
that of HSV-1 B capsids. This is illustrated from the
radial density plots shown in Fig. 2. HCMV has an
FIG. 4. (A) Enlarged view of a HCMV1 hexamer from an average outer radius of 65 nm compared with 62.5
icosahedral 2f axis. (B) Enlarged view of a HCMV1 pentamer from
an icosahedral 5f axis. Adjacent triplexes can also be seen at the
nm for HSV-1. The internal radius of the capsid was
base of each capsomer. estimated using the peak from the radial density
plot (Fig. 2) corresponding to the floor of the shell in
Figs. 3C and 3D (HCMV, 50 nm; HSV-1, 47.5 nm).
tip of each hexon subunit is topped by a rod-shaped The average height of the capsomers is 15 nm in both
protrusion (Figs. 3A, 3C, 4A), so the hexon looks like cases. In addition the maximum hexon diameter is
an open flower with six petals (Figs. 3A, 4A). In similar in both structures (13.7 nm, Figs. 3C, 3D).
contrast, the penton subunit tips are more pointed, However, a distinct difference is the relative tilt
giving a triangular cross section (Figs. 3A, 3C, 4B). between adjacent hexons. For instance, the angle
between the hexon on the 2f axis (9 o’clock, Figs. 3C, 3D)
Triplexes and the adjacent hexon is 9.5° in HCMV but only 5° in
The triplexes are the structures found at the local HSV-1. Consequently, the separation between the hex-
threefold axes of symmetry, interacting with the ons at the base, measured from the center of one hexon
hexon and penton walls (Figs. 3A, 3C, 4). The to the center of the next, is 14.7 nm in both structures.
triplexes do not appear to be threefold symmetric However, at the tip of the hexons, it has increased to
despite their position. Instead they vary depending 17.9 nm in HCMV and only 15.8 nm in HSV-1, directly
on the location within the asymmetric unit (Figs. 3A, accounting for a change in capsid diameter.
4). The most striking triplexes are those interacting The tips of the HSV-1 hexons that have been
with the pentons, where the triplex forms a buttress identified as a single protein species, VP26 (Booy et
against the penton wall (Figs. 3A, 3C, 4B). al., 1994; Trus et al., 1995; Zhou et al., 1995), are not
as prominent as those of HCMV at this resolution
Floor of the Capsid (Figs. 3, 4A). Those on the HCMV hexons are similar
The floor of the capsid is seen as a peak of density in length, but are 33% thinner (Figs. 3C, 3D); the
in the radial profiles (Fig. 2) at a radius of 50 nm in choice of contour level did not appreciably affect the
HCMV. This floor is penetrated by holes at the base appearance or dimensions of these features. The
of each capsomer and underneath the triplexes (Fig. HSV-1 pentons lack VP26, giving the pentons a
3C). The thinnest part of the shell occurs between distinctive top compared with the hexons. In HCMV,
the triplexes. the penton tips are also distinct from those of the
hexons (Fig. 4). This may reflect a difference in
Internal Details composition between the hexons and the pentons
The scaffold core is a very strong feature in the due to the SCP, or a conformational difference be-
HCMV micrographs (Fig. 1). However, it is not tween the hexameric form and the pentameric form
evident in the reconstructions (Fig. 3C). Inside the of the MCP.
capsid, there is only a low signal from icosahedrally The final difference between the two capsids is the
ordered mass above the background noise level, distribution of the scaffold core, which can be seen
which varies between different HCMV reconstruc- from the radially averaged profiles (Fig. 2). The
tions, suggesting that it is not significant (data not profile of the HSV-1 B capsid agrees well with that of
shown). Although the density from the scaffold pro- Zhou et al. (1998b). However, the average density falls
teins does not reveal an icosahedrally ordered struc- off at radii of 22 nm in HSV-1 and 38 nm in HCMV.
ture (Fig. 3C), we can still estimate the extent of the
DISCUSSION
majority of the scaffold from the radial density plot
(Fig. 2). This gives an average scaffold core radius of The overall architectural design of the herpesvirus
38 nm The dips seen at low radii (less than 5 nm) are capsid has been conserved among different subfami-
probably artifacts of the Fourier Bessel procedures, lies. However, our studies have demonstrated that
as analysis of the aligned raw data did not show limited changes can be made to the capsid structure
similar fluctuations. by virus-specific differences in the component proteins.
STRUCTURE OF HUMAN CYTOMEGALOVIRUS 75

The HCMV capsid is made up of hexamers and smaller channel catfish virus were reported to have
pentamers arranged on a T 5 16 lattice. By analogy similar genome packing densities (Booy et al., 1996).
with HSV-1, we expect that the major capsid protein Alternatively HSV-1 may underutilize its packaging
(MCP) forms the major part of these structures and capacity like bacteriophage l, which can package
that the smallest capsid protein (SCP) forms the tips DNA 9% larger than its genome without affecting
of the hexons. The minor capsid protein (mCP) and viability (Weil et al., 1972). A third possibility is that
the mCP-binding protein (mC-BP), which associate an expansion of the HCMV capsid is associated with
together in a ratio of 2:1, are analogous to the triplex DNA packaging. B capsids from simian CMV have
proteins of HSV-1 and probably form the equivalent been estimated to have a diameter 7% smaller than
structures seen in the HCMV reconstruction at the that of A capsids when examined in thin sections of
positions of local threefold symmetry (Fig. 4). infected cell nuclei (Lee et al., 1988). Studies of the
One of the motivating questions for performing DNA-containing capsid are required to address these
this study was: How does the capsid of HCMV issues in more detail. We have endeavored to isolate
package a genome that is 60% larger than that of such capsids from both virions and infected cells, but
HSV-1? There is, as predicted from a comparative invariably ended up with damaged, empty capsids.
study between HSV-1 and channel catfish virus This implies that HCMV is more fragile than HSV-1.
(Booy et al., 1996), no change in the T number of the In conclusion, this preliminary study of HCMV
capsid to accommodate the larger genome; however, emphasizes the similarities between evolutionary
there is an increase in the capsid volume. The distinct herpesviruses. It also supports the idea that
internal radius of the capsid was estimated using the although the three-dimensional structures of the
peak from the radial density plot which corresponds capsid proteins are similar at the gross level, we can
to the floor of the shell (HCMV, 50 nm; HSV-1, 47.5 expect changes in the interactions between mono-
nm) because the edge of the shell density is harder to mers at the atomic level, giving rise to differences in
estimate. Assuming a sphere, this gives a volume spacing between capsomers.
ratio of 1.17 for HCMV compared with HSV-1. This is Dr. Hong Zhou is thanked for providing a reconstruction of
much smaller than the ratio of the genome lengths HSV-1 B capsids. Dr. Frazer Rixon is thanked for helpful discus-
(1.51) of the two virus strains used in this study sions. Dr. Stephen Fuller kindly provided his programs, as did
[HCMV AD169, 230 kb (Dargan et al., 1997); HSV-1 Felix deHaas and Ralph Heinkel. Ilaria Ferlenghi and Erica
Mancini are thanked for help with scanning of the micrographs.
strain 17, 152 kb (McGeoch et al., 1988)]. Interest- This work was funded by the U.K. Medical Research Council.
ingly, HCMV assembles this larger shell with pro-
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