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Journal of Virology, August 1999, p. 6759-6768, Vol. 73, No. 8
0022-538X/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Structure of Adenovirus Complexed with Its
Internalization Receptor,
v
5 Integrin
Charles Y.
Chiu,1
Patricia
Mathias,2
Glen R.
Nemerow,2,* and
Phoebe L.
Stewart1,*
Department of Molecular and Medical
Pharmacology, Crump Institute for Biological Imaging, University of
California
Los Angeles School of Medicine, Los Angeles, California
90095,1 and Department of
Immunology, The Scripps Research Institute, La Jolla, California
920372
Received 19 February 1999/Accepted 21 April 1999
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ABSTRACT |
The three-dimensional structure of soluble recombinant integrin
v
5 bound to human adenovirus types 2 and 12 (Ad2 and
-12) has been determined at ~21-Å resolution by cryoelectron
microscopy (cryo-EM). The
v
5 integrin is known to
promote Ad cell entry. Cryo-EM has shown that the integrin-binding RGD
(Arg-Gly-Asp) protrusion of the Ad2 penton base protein is highly
mobile (P. L. Stewart, C. Y. Chiu, S. Huang, T. Muir, Y. Zhao, B. Chait, P. Mathias, and G. R. Nemerow, EMBO J. 16:1189-1198, 1997). Sequence analysis indicated that the Ad12 RGD
surface loop is shorter than that of Ad2 and probably less flexible,
hence more suitable for structural characterization of the Ad-integrin
complex. The cryo-EM structures of the two virus-receptor complexes
revealed a ring of integrin density above the penton base of each virus
serotype. As expected, the integrin density in the Ad2 complex was
diffuse while that in the Ad12 complex was better defined. The integrin consists of two discrete subdomains, a globular domain with an RGD-binding cleft ~20 Å in diameter and a distal domain with
extended, flexible tails. Kinetic analysis of Ad2 interactions with
v
5 indicated ~4.2 integrin molecules bound per
penton base at close to saturation. These results suggest that the
precise spatial arrangement of five RGD protrusions on the penton base
promotes integrin clustering and the signaling events required for
virus internalization.
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INTRODUCTION |
The integrins comprise a large
family of heterodimeric cell surface receptors that mediate biological
processes as diverse as cell-cell communication, cell movement and
adhesion, leukocyte trafficking, and even short-term memory in
Drosophila (20, 25). Because of their prominent
role in cellular adhesive and promigratory interactions, integrins are
also involved in a number of disease states, including tumor growth and
metastasis, osteoporosis, and the development of atherosclerotic
lesions (21). There are 16 known
and 8 known
subunits that combine to form at least 22 distinct
-
heterodimers
(24). Integrins are able to recognize both cell surface and
extracellular matrix ligands, with ligand-binding specificity conferred
by the pairing of different subunits.
The regulation of integrin-mediated signal transduction is complex and
is governed by a number of factors, including ligand occupancy,
receptor conformation and/or aggregation, and interaction with divalent
metal cations (22, 23, 33). Cell signaling by integrins
results in the colocalization of cytoskeleton-associated proteins, such
as talin and
-actinin, as well as tyrosine phosphorylation and
activation of downstream effector kinases (27). Efficient signal transduction requires both receptor occupancy and clustering (36), which can be induced by multivalent ligands, such as
many extracellular matrix proteins or the penton base protein of
adenovirus type 2 (Ad2) (31, 32).
The two subunits of the integrin heterodimer are known to noncovalently
interact with each other at their N termini to form a large
extracellular head. This globular domain is connected to two separate
tails that cross the plasma membrane and possess short cytoplasmic
signal transduction sequences at their C termini. The large size of the
integrin heterodimer (~250 kDa), coupled with the presence of
multiple domains and numerous glycosylation sites, has made
high-resolution structural studies difficult. To date, the only crystal
structures of integrin solved are those of the
-chain "inserted"
subdomains (i.e., the I domain or A domain) of
L
2,
M
2, and
2
1, which reveal a novel
metal cation binding region and a potential ligand-receptor
coordination site (18, 30, 39). Crystallographic
characterization of an RGD ligand-integrin complex may be hindered by
the observed flexibility in integrin-binding RGD loops (4, 17,
43). Overall dimensions of the entire integrin heterodimer have
been estimated from rotary-shadow, negative-stain, and freeze-fracture
electron microscopy (EM) (12, 37, 41, 48). The reported
dimensions of the globular head are in the range of 80 by 80 to 80 by
120 Å.
In addition to their normal role in mediating cellular adhesion,
integrins have been usurped by a number of viral and bacterial pathogens in order to gain entrance into host cells. For example, the
vitronectin binding
v
3 and
v
5
integrins are internalization receptors for human Ad (8,
49). Following initial Ad attachment via the fiber receptor
(9), there is rapid internalization of the virus into
clathrin-coated vesicles mediated by penton base association with
integrin
v
3 or
v
5. Ad endocytosis
also requires cell-signaling events mediated by the activation of
PI3-kinase (32) and the Rho family of small GTPases
(31). These signaling molecules stimulate polymerization of
cortical actin filaments needed for virus uptake into cells.
The Ad penton base protein consists of five polypeptide subunits, each
containing an integrin-binding RGD (Arg-Gly-Asp) peptide sequence
(49). The RGD motif is highly conserved in multiple Ad
serotypes and is found in a number of cell matrix and adhesion proteins, such as fibronectin and vitronectin, that also bind integrins. The presence of a conserved RGD motif in different Ad
serotypes, as well as competition studies with function-blocking monoclonal antibodies (MAbs) to
v integrins, indicate
that different Ad serotypes use a common pathway for entry into host
cells (35). Sequence alignment of four different Ad penton
base proteins reveals that the RGD residues are positioned in the
middle of a highly variable stretch, with a length ranging from ~20
residues for Ad12 to more than 80 residues for Ad2. A cryo-EM
reconstruction of human Ad2 complexed with a neutralizing Fab fragment
from an RGD-specific MAb (named DAV-1) localizes the RGD sequence to a highly mobile surface protrusion on the penton base protein
(43). The mobility of RGD loops has been postulated to be a
structural feature that facilitates integrin binding.
The ectodomain, or extracellular portion, of
v
5
integrin has been expressed as a soluble recombinant molecule
(34), enabling structural studies of Ad-integrin
interactions by cryo-EM. Here we present the structures of the
Ad2-integrin and Ad12-integrin complexes at ~21-Å resolution. We
hypothesized that the smaller and less flexible RGD protrusion of Ad12
would be advantageous for structural characterization of the complex.
Our results reveal a well-defined ring of integrin bound to the Ad12
penton base and shed further light on the mechanisms of integrin interactions.
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MATERIALS AND METHODS |
Production and kinetic analyses.
Recombinant baculovirus
vectors encoding soluble
vFos and
5Jun
integrin subunits were constructed as previously described (34). The secreted integrin heterodimer was isolated by
immunoaffinity chromatography with the P1F6 anti-
v
5
MAb. Eluted fractions containing the ~155- to 100-kDa integrin
heterodimer were pooled and concentrated (C-100 microconcentrator;
Amicon) to 2 mg/ml (Bio-Rad protein assay with bovine serum albumin as
a standard) and stored at
80°C. Real-time measurements of integrin
association with intact Ad2 particles were carried out with an
automated biosensor (BIAcore 2000; Pharmacia). A similar approach was
used to measure the precise kinetics of soluble intercellular adhesion
molecule-1 interaction with human rhinovirus (13). The A18
MAb, which recognizes the distal-domain portion of the Ad2 fiber
protein, was used to "capture" intact virus particles onto
biosensor chips. Carboxymethyl-dextran coated biosensor chips (CM5
research grade; Pharmacia) were activated with
N-hydroxysuccimide and
N-ethyl-N'-(dimethylaminopropyl)carbodiimide for 7 min, and
a 135-µg/ml solution of A18 MAb in 10 mM sodium acetate buffer, pH
4.4, was passed over the surface at a flow rate of 5 µl/min for 4 min. Nonspecific sites were quenched by addition of 1 M
ethanolamine-HCL, pH 8.5, for 7 min. Following covalent coupling of the
A18 MAb, 10 µl of 140 µg of purified Ad2/ml in 10 mM
Tris-HCl-buffered saline, pH 7.4, was passed over the biosensor chip at
a flow rate of 1 µl/min and allowed to equilibrate. Various
concentrations of the DAV-1 anti-penton base MAb (6 to 500 nM) or the
purified
v
5 integrin (0.1 to 8.0 µM) in the
presence or absence of divalent metal cations were passed at 40 µl/min over a blank biosensor chip or a chip containing the
immobilized Ad2 particles. The surface was regenerated after each
binding interval by using 15 µl of 50 mM diethylamine, pH 10.0, at a
flow rate of 100 µl/min. Kinetic binding data, including association (ka) and dissociation
(kd) rate constants, were determined with BIAevaluation software version 3.0. Stoichiometric data were obtained by observing changes in surface plasmon resonance at saturation. Molecular masses of 250 kDa for integrins, 150 kDa for DAV-1, and
1.5 × 105 kDa for Ad2 particles were used in
calculations for stoichiometry.
Cryo-EM and negative-stain EM.
For negative-stain EM, the
soluble recombinant
v
5 integrin was concentrated to
~275 µg/ml, negatively stained with 2% uranyl acetate, and
examined with a Philips CM120 transmission EM. For cryo-EM, the volumes
of the purified Ad2 and Ad12 virus preparations were adjusted to
achieve a concentration of ~200 µg/ml, which we have found to be
optimal for well-spaced particles in the cryogrid. To generate the
Ad-integrin complexes, recombinant
v
5 and the Ad
particles were incubated at a molar ratio ranging from 5:1 to 7:1
integrins per viral binding site in Tris (pH 8.1)-1 mM Ca2+-1 mM Mg2+ buffer for 12 h on ice
(0°C). Cryoplunging of Ad2-integrin complexes, Ad12-integrin
complexes, and the corresponding unbound particles was performed
according to well-established procedures (3). Holey carbon
grids were prepared by layering Triafoil plastic film with 0.1- to
1-µm-sized holes on 400-mesh copper grids. A 3-µl droplet of
concentrated sample was placed on a glow-discharged holey carbon grid,
blotted for 10 s, and plunged immediately into ethane slush
chilled by liquid nitrogen. The frozen grid was then transferred under
liquid nitrogen to a prechilled Gatan 626 cryotransfer holder and
inserted into a CM120 transmission EM equipped with cryoaccessories.
Digital micrographs of the virus particles were collected with a Gatan
slow-scan charge-coupled device camera (1,024 by 1,024 pixels) under
low-dose conditions (<20 electrons/Å2) at three discrete
levels of defocus (
0.5,
1.0, and
1.5 µm). The variation in
defocus within a set of micrographs collected with the same nominal
value is approximately ±5%, as estimated from the reproducibility of
setting the focus visually. Experimentally, we have found that
17-Å-resolution reconstructions can be achieved even with slight
variations in defocus value within a set of images taken with the same
nominal defocus value (42). The Ad images were collected
with a nominal magnification of ×45,000, corresponding to an effective
magnification of ×59,000 at the level of the charge-coupled device
camera. The image pixel size, considering the effective magnification,
was 4.1 Å and was confirmed by calibration with a catalase crystal.
Image processing.
The QVIEW software package was used to
extract individual particle images as 400- by 400-pixel fields
(40). Preliminary image processing with QVIEW involved
exclusion of density from nearby particles and the carbon edge, planar
background subtraction, and application of a circular mask. All
subsequent processing steps were performed in the context of the IMAGIC
image-processing system (47). Four sets of 396-, 436-, 243-, and 285-total-particle images of Ad2, Ad12, Ad2-integrin, and
Ad12-integrin, respectively, were collected. The number of Ad-integrin
particle images was limited by the amount of soluble recombinant
v
5 available. The sets were partitioned according to
defocus value, and each subset was then normalized as well as
translationally aligned to a calculated reference (the rotationally
averaged sum of the input images). Next, the initial Euler
orientational angles for the particle images were determined via the
technique of angular reconstitution, assuming icosahedral symmetry.
Correction for the microscope contrast transfer function (CTF) was
carried out for each subset with a deconvolution program, 2D-DECON,
written in FORTRAN (15, 42). The CTF was modeled in Fourier
space as a sinusoidal function multiplied by an exponentially decaying
"envelope" (44). The parameters used for the modeled CTF
equation (spherical abberation constant [Cs], 2 mm; fraction of
amplitude contrast, 0.1; kV, 120; decay constant, 20 nm2;
Fermi filter resolution cutoff, 8.2 Å; filter width, 3 Å; defocus,
0.5 to
1.5 µm) were selected to minimize CTF ringing effects as
observed in the particle images. These parameters also best removed the
defocus ringing effects as observed in the central slice of an Ad
reconstruction calculated from images of a single defocus value.
Deconvolution was performed by dividing the Fourier amplitudes of the
particle images by the CTF, assuming a threshold of 0.05 to prevent
division by zero at the CTF nodes. The deconvolved particle images were
then recombined, and preliminary three-dimensional reconstructions were
calculated with IMAGIC by exact filtered back projection (Hamming
filter factor, 0.75).
Anchor sets of projections from initial particle reconstructions were
used to progressively refine the Euler angles of the
input images. In
anchor set refinement, the sinograms of projections
spanning the
asymmetric unit are compared with the sinogram of
the current
projection and the sinogram correlation function is
calculated to find
a better particle orientation (
38,
47).
We have modified
this procedure slightly by considering only nearby
orientations within
the asymmetric unit (nearest-neighbor anchor
set refinement) when
calculating the sinogram correlation function.
This conserves
processing time and allows a finer-step search
for particles whose
orientations are nearly correct. Further translational
refinement was
also carried out by translating the input images
to maximize the
cross-correlation coefficients with their corresponding
projections.
The cycles of orientational and translational refinement
were continued
until there was no longer any improvement in the
resolution of the
final structure as assessed by Fourier shell
correlation (FSC).
Typically, convergence occurred after two to
three
iterations.
Particle images showing the largest percent error were removed from the
Ad2 and Ad12 sets to match the number in the corresponding
Ad2-integrin
and Ad12-integrin complex sets. Thus, the final reconstructions
were
calculated from 243 particle images for Ad2 and Ad2-integrin
and 285 particle images for Ad12 and Ad12-integrin with a 4.1-Å
voxel. The
resolution of the final reconstructions was evaluated
by first applying
a "soft" mask with a Gaussian fall off at the
edges to select just
the ordered viral capsid (
42). The resolution
of the
reconstructions was assessed by FSC (
10,
16) and the
Fourier
shell phase residual (FSPR) (
38,
46). The resolution
indicated by the 0.5 FSC criterion and the 45° FSPR threshold
was 20 to 22 Å for all four reconstructions. For purposes of difference
imaging, all reconstructions were first filtered to 22-Å resolution
and then normalized based on the strong capsid density. Difference
imaging of the filtered and scaled maps isolated the density
corresponding
to
v
5 integrin bound to Ad2 and Ad12.
Specifically, the uncomplexed
Ad reconstruction was masked at the
isosurface threshold chosen
for the viral capsid and subtracted from
the corresponding Ad-integrin
complex
reconstruction.
Due to computational limitations, the maximum size of the reconstructed
density map was limited to (256 pixels)
3. This corresponded
to an outer diameter of (1,050 Å)
3 with a pixel size of
4.1 Å and truncated a portion of the integrin
density. Additional
(200-pixel)
3 maps were thus calculated, with an
interpolated pixel size of
8.2 Å and a maximum diameter of (1,640 Å)
3 to encompass all of the integrin. The 200
3
interpolated maps were found by FSC to have resolutions of ~24
Å.
Structural analysis.
Isosurface representations of the
scaled density maps were displayed with the AVS visualization software
package (Advanced Visualization Systems, Inc.). The isosurface value
for the viral capsid was selected to yield a continuous, nonholey
capsid surface. The weak density in the Ad2 and Ad12 penton base
protrusions was contoured at a level just above noise. For the
v
5 density in the Ad12 complex reconstruction which
included both integrin domains, the isosurface value was chosen to
correspond to the molecular mass of five bound integrin heterodimers
(250 kDa × 5 = 1,250 kDa). For the
v
5
density in the Ad12 complex reconstruction with just the integrin
proximal domain, the integrin isosurface was chosen to match the
appearance of the proximal domain in the full integrin. For the
v
5 density in the Ad2 complex reconstruction, two
isosurface values were selected: one chosen to match the level of the
better-defined Ad12 integrin density and the other set just above the
noise level.
An occupancy estimate for the integrin in the Ad12 complex was
determined from the average of three measurements, assuming
100%
occupancy for the penton base protein. The first method involved
summing up all of the density within the chosen contour for the
integrin, dividing by the molecular mass of five bound soluble
integrin
molecules, and comparing this ratio with that found for
the penton
base. Since the penton base is difficult to isolate
from the viral
capsid, we estimated the sum of the density by
multiplying the mean
density within the approximately cropped
penton base by the expected
volume. The second approach involved
the ratio of the average density
for these two protein components,
and the third was based on the ratio
of the maximum density. Structural
flexibility in the Ad2 RGD loop
resulted in
v
5 density that
was diffuse and spread
out over a larger volume. Thus, only the
first measurement was used to
estimate the integrin occupancy
in the Ad2 complex. The length of the
variable region flanking
the RGD motif in the Ad2 and Ad12 penton base
sequences was determined
by a BLAST search multiple-alignment procedure
(
5,
11). The
alignment was carried out on the penton base
sequences of five
different Ad serotypes obtained from the SWISS-PROT
and TREMBL
databases.
 |
RESULTS |
Kinetic analysis of integrin and antibody associations with Ad
particles.
Structural analysis of integrins has been limited by an
inability to purify sufficient amounts of the native receptor from mammalian cells. In addition, integrins isolated from normal human tissues frequently aggregate via their hydrophobic transmembrane domains, thus hindering precise measurement of integrin-binding properties. To circumvent these problems, we expressed the entire ectodomain of integrin
v
5 as a soluble protein in
insect cells. The intact integrin heterodimer retains the ability to
bind to its natural ligand, vitronectin, as well as to the penton base protein of several different Ad serotypes (34).
Negative-stain EM of the soluble recombinant
v
5
integrin revealed >99% of the heterodimers to be in a monodispersed
form in the absence of ligand.
In order to determine the stoichiometry and kinetics of soluble
integrin association with intact virus particles, we performed
binding
studies with an automated biosensor (BIAcore 2000; Pharmacia).
Ad2
particles were indirectly linked to a biosensor chip via a
MAb (A18)
specific for the distal portion (knob) of the Ad2 fiber
protein.
Various amounts of soluble
v
5 integrin were passed
over immobilized virus particles (Fig.
1). The association
(
ka)
and dissociation
(
kd) rate constants and stoichiometry were
determined
by monitoring the change in surface plasmon resonance over
time
(Table
1). Analysis of the binding
site at close to saturating
conditions indicated ~50 integrin
molecules bound to each adenovirus
particle, or ~4.2 integrin
molecules bound per penton base protein.
Binding of the integrin also
required the presence of divalent
metal cations, as its association
with virus particles was completely
abolished in the presence of 20 mM
EDTA.

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FIG. 1.
BIAcore sensorgrams of soluble v 5
integrin or DAV-1 MAb binding to Ad2 particles. Various amounts of
soluble v 5 integrin or antibody (1, 500 nM integrin;
2, 50 nM DAV-1 MAb; 3, 2 µM integrin; 4, 4 µM integrin; 5, 8 µM
integrin, 6, 500 nM integrin plus 20 mM EDTA) were passed over a
biosensor chip containing immobilized Ad2 particles, and the
association and dissociation rates were measured in real time with a
BIAcore 2000 biosensor as described in Materials and Methods. For
clarity, only the sensorgram of DAV-1 MAb binding (blue line) at
saturating conditions is shown. The relatively large bulk-flow response
seen in sensorgram 6 is due to the presence of 20 mM EDTA. This
response does not represent specific integrin binding, as indicated by
the absence of resonance units (RUs) following dissociation.
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TABLE 1.
Association and dissociation rate constants, affinity,
and stoichiometry of antibody and v 5 integrin
interaction with Ad2 particlesa
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This experiment was repeated with a penton base MAb (DAV-1) directed
against the integrin-binding site (IRGDTFATR) (
43).
Only
~1.7 molecules of the DAV-1 MAb were calculated to bind to
each
penton base protein of Ad2. Due to the 50-fold-higher affinity
of the
DAV-1 MAb (1.4 nM) over the integrin (73 nM), it was much
easier to
reach saturation with the MAb. It is unknown whether
the DAV-1 MAb
binds monovalently or bivalently to the penton base;
however, it is
known that it does not neutralize the virus (
43).
This is
consistent with our current stoichiometry measurement,
which shows the
MAb does not bind to all five RGD sites on the
penton base. In
contrast, four to five
v
5 integrin molecules
can
clearly associate with a single penton base, as shown by our
stoichiometry
measurements.
Cryo-EM structures of Ad2 and Ad12.
Three-dimensional image
reconstructions of Ad2 and Ad12 were calculated to perform a detailed
comparison of the RGD-containing penton base protrusions as well as to
allow difference imaging with the Ad-integrin complex structures. The
resolution of the Ad2 reconstruction was 21 Å as assessed by the
commonly used FSC (10, 16) and FSPR methods (38,
46) (Fig. 2A and B). The resolution
of the Ad12 reconstruction was similar at 22 Å. An independent
resolution estimate was also made for Ad2 by comparison of the cryo-EM
density with the filtered crystallographic structure of the Ad2 major
capsid protein hexon (6). This comparison confirms that the
cryo-EM resolution is at least 21 Å (Fig. 2C and D). The three towers
of the cryo-EM hexon appear broader (65 Å) than the filtered
crystallographic hexon (30 Å). The broad towers represent a real
structural feature that is apparent when the crystallographic hexon is
filtered to 15- to 17-Å resolution (42).

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FIG. 2.
Resolution assessment of the Ad2 cryo-EM reconstruction.
(A) Plot of the FSC (solid line) and the corresponding 23.2 (3 ,
adjusted for icosahedral symmetry) significance threshold curve (dashed
line) (38). (B) Plot of the FSPR. Both the FSC and FSPR were
calculated from soft masked reconstructions that only included the
ordered protein capsid without the disordered fiber and core density.
(C) One hexon from the Ad2 cryo-EM reconstruction filtered to 21 Å,
the resolution indicated by the 0.5 correlation point of the FSC and
the 45° criterion of the FSPR. (D) The crystallographic structure of
the Ad2 hexon (6) filtered to 21-Å resolution. The density
maps shown in panels C and D are color coded by height. The
magnification of the cryo-EM structure was adjusted by ~5% for the
best match with the filtered crystallographic hexon. The scale bar is
25 Å.
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Overall, the reconstructions showed that Ad2 and Ad12 particles were
similar, with only minor structural variations observed
at the tops of
the hexon towers and penton base protrusions (Fig.
3A to
C). A BLAST alignment of the Ad2 and Ad12
hexon sequences
indicates that there are 45 fewer residues in the tower
region
of the Ad12 hexon, consistent with the smaller appearance of the
Ad12 hexon towers. The fiber is truncated in both reconstructions
as
only the lower portion of the flexible shaft follows icosahedral
symmetry. Close inspection of the penton base protrusions in the
two
serotypes revealed a noticeable size difference. When the
penton base
was contoured at a level to show only the strong,
well-defined capsid
density, the protrusions of the two serotypes
appeared similar.
However, when contoured at a level just above
noise, the Ad2 protrusion
showed much more weak density (Fig.
3C). For Ad2, the weak density
extended ~15 Å outwards from the
well-defined portion of the
protrusion, whereas for Ad12, the
weak density extended only ~6 Å.
Moreover, the total volume encompassed
by a single Ad2 protrusion,
including the weak density, is ~26,100
Å
3, while the
corresponding volume for Ad12 is only ~17,500 Å
3.
Interestingly, this difference in volume corresponds to the
volume of
~58 amino acid residues. This is in close agreement
with the
observation that there are 62 additional residues flanking
the RGD
motif in Ad2 (Fig.
3D). The finding of additional weak
density above
the Ad2 penton base protrusion implies the presence
of a more flexible
RGD loop.

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FIG. 3.
Cryo-EM reconstructions of Ad2 (left) and Ad12 (right)
at ~21-Å resolution. (A) Ad capsids viewed along an icosahedral
threefold axis. The penton base proteins at the icosahedral vertices
are shown in yellow, the reconstructed portion of the flexible fibers
are in green, and the remaining capsid density is in blue. (B) Side
views of the external portion of the penton base contoured at a level
corresponding to the strong capsid density. (C) Enlargements of a
single penton base protrusion at two isosurface levels, one just above
noise (transparent red) and the other showing well-defined density
(yellow). (D) The lengths of the variable regions flanking the RGD
sequence (red) in Ad2 and Ad12 are obtained from sequence alignment of
five different Ad serotypes. The scale bars are 100 (A) and 25 (B and
C) Å.
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Cryo-EM structures of Ad complexed with soluble
v
5 integrin.
To ensure maximal occupancy of the
viral RGD-binding sites by integrin molecules, an ~6-fold molar
excess of
v
5 integrin per RGD-binding site was mixed
with concentrated Ad2 or Ad12 virus preparations. Ca2+ and
Mg2+ ions were added to promote and stabilize
ligand-receptor complex formation. Occasionally, cryo-EM images of the
virus-receptor complexes revealed extra density near the Ad fibers
(Fig. 4A). Given the low signal-to-noise
ratio in cryo-electron micrographs, it was difficult to discern any
differences in integrin binding between Ad2 and Ad12 in the raw
particle images. Three-dimensional reconstructions of both Ad2 and Ad12
complexed with integrin were calculated to resolutions of 20 and 21 Å,
respectively. Due to computational limitations, it was necessary to
interpolate the density maps in order to visualize the full extent of
the integrin. These interpolated maps (Fig. 4B to D) spanned the
maximum diameter of the Ad-integrin complexes, ~1,200 Å, and had
resolutions of ~24 Å.

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FIG. 4.
Cryo-EM reconstruction of the Ad2-integrin (left) and
Ad12-integrin (right) complexes at ~24-Å resolution. (A)
Representative particle images with arrows indicating regions of
density attributed to v 5 integrin. (B) Ad complexes
viewed along an icosahedral threefold axis. The color scheme is the
same as in Fig. 3A, with v 5 integrin density shown in
red. (C) Side views of the penton base, fiber, and integrin. The
Ad12-integrin density is contoured at a level corresponding to five
bound v 5 heterodimers. The Ad2-integrin density is
contoured at the same level (solid red) and just above noise
(transparent red). (D) A cropped view of the vertex regions of the Ad
complexes showing connections between the integrin and the penton base
via the RGD protrusions (arrows). The slice plane is color coded on the
basis of density, with the strongest density values shown in red and
the weakest in blue. The scale bars are 100 Å.
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The structure of soluble
v
5 integrin bound to the
Ad penton base.
Difference imaging between the Ad-integrin
complexes and the corresponding uncomplexed reconstructions revealed
that bound integrin molecules form a ring-like cluster above each
penton base protein (Fig. 4B). Enlarged views of the vertex region show that the integrin density in the Ad2 complex extends farther from the
surface of the viral capsid and has a larger volume than in the Ad12
complex (Fig. 4C). The
v
5 integrin in the Ad12
complex was contoured to enclose a volume equivalent to five bound
molecules, assuming a molecular mass of 250 kDa for an integrin
heterodimer. The integrin density in the Ad12 complex consists of a
globular proximal domain and a tail-like distal domain, where proximal and distal are defined with respect to the virus rather than the cell
surface. While the Ad12 proximal domain displayed well-defined density,
the distal domain showed weaker, more diffuse density suggestive of
flexible tails. The proximal and distal integrin domains in the Ad2
complex are disconnected at an equivalent isosurface (Fig. 4C).
Connections were only observed when the isosurface level was further
lowered to just above noise (Fig. 4C). At this lowered isosurface
level, the volume of the integrin in the Ad2 complex is 150% of that
expected for five bound integrin heterodimers. The integrin in the Ad2
complex also has weaker density values than that in the Ad12 complex,
as shown in crop planes through the vertex regions (Fig. 4D). In both
complex structures, the integrin is clearly connected to the penton
base via the protrusions and appears to bind at an ~45° angle with
respect to the fivefold fiber axis.
The finding of stronger, more compact integrin density in the Ad12
complex cannot be explained by differences in ligand-receptor
affinities. Measurements of
v
5 interaction with Ad2
and Ad12
in solid-phase binding assays indicated that integrin has a
higher
binding capacity for Ad2 than for Ad12 (
34).
Integrated density
measurements of the reconstructions showed nearly
100% occupancy
of the integrin receptor for Ad2 but only ~73%
occupancy for Ad12.
We surmise that the longer and more mobile RGD
region in Ad2 allows
greater flexibility for the bound integrin than
does the shorter
RGD region in Ad12, thus explaining the weaker, less
compact integrin
density in the Ad2 complex despite higher occupancy.
The flexibility
of the RGD-binding site in Ad2 prevents a detailed
structural
analysis of the integrin in the Ad2 complex, as the diffuse
integrin
density is a result of averaging over multiple orientations.
In
contrast, the well-defined integrin density in the Ad12 complex
is
consistent with a constrained orientation for at least the
globular
proximal domains of the bound
integrin.
Ring structure formed by integrin-proximal domains.
Further
structural analysis of the
v
5 integrin was carried
out on the Ad12 complex reconstruction. The integrin proximal domains
were observed to form a ring of density, shown color coded by height in
Fig. 5. The integrin
ring has a height of 80 Å and a maximum outer diameter of 200 Å and
appears to be segmented into five regions (Fig. 5A). The side view in
Fig. 5C shows five columns of density that connect the proximal domain
to the more diffuse density in the distal domain. The tilted view in
Fig. 5D reveals that the inner surface of the integrin ring is sloped from an inner diameter ranging from 70 Å at the top to 130 Å at the
base. The bottom view in Fig. 5E displays five clefts, ~20 Å in
diameter, where the penton base protrusions bind (see Fig. 7).

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FIG. 5.
Integrin ring from the Ad12- v 5
complex at ~21-Å resolution. The ring is formed by associations
between the RGD-binding proximal domains. (A to E) Five views of the
height-color-coded ring from top to bottom. Note that the top surface
has five columns of density (red) that connect the proximal domains to
the more flexible distal domains (not shown). The bottom-surface view
shows five clefts (arrows), each ~20 Å in diameter, that bind the
RGD-containing protrusions of the penton base protein. The scale bar is
100 Å.
|
|
Successive slices through the vertex region of the Ad12-integrin
complex show the interaction between the integrin and the
penton base
(Fig.
6). In slice plane 1, only density
corresponding
to the penton base and hexon towers is observed. The
remaining
slice planes show the molecular edge of the integrin outlined
in black. In slice plane 3, the five penton base protrusions are
observed to contact the sloping inner surface of the integrin
ring.
Note also that in this slice there is a clear separation
of the
integrin ring into five regions. However, at planes further
from the
viral surface, there are large regions of contact between
neighboring
integrin molecules (planes 4 to 6). Close apposition
of adjacent
receptor molecules is also noticeable in the top-surface
view of the
integrin ring (Fig.
6A).

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FIG. 6.
Integrin ring in association with the Ad12 capsid. (A)
Side- and top-surface views. (B) Slice planes through the integrin
density perpendicular to an icosahedral fivefold symmetry axis. The
heights of the slice planes are indicated by numbered lines in panel A. The color scheme for the individual proteins is as shown in Fig. 4B.
Stronger density values are represented by darker shades, and weaker
density values are represented by lighter shades. The black lines in
slice 3 designate the boundary for the extracted model of one integrin
proximal domain displayed in Fig. 7. The scale bars are 100 Å.
|
|
One-fifth of the integrin ring formed by the proximal domains is shown
extracted and in context with the Ad12 penton base
in Fig.
7A. We present this as a model for the
proximal domain
of a single integrin heterodimer. The BIAcore
measurements indicate
that division of the density into five parts is
reasonable given
that integrin molecules were capable of binding to all
five RGD
sites on the Ad2 penton base. The extracted integrin density
enables
visualization of a single penton base protrusion binding within
a cleft on the inner sloping surface of the proximal domain (Fig.
7B
and C). The protrusion is known to contain the RGD motif from
previous
cryo-EM studies of Ad2 complexed with an RGD-specific
Fab fragment
derived from a monoclonal antibody (DAV-1) (
43).

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FIG. 7.
Model for the interaction between the integrin proximal
domain and the Ad12 penton base protein. One-fifth of the integrin ring
density is shown extracted along estimated boundaries to model the
proximal domain of a single v 5 heterodimer. (A) The
modeled proximal domain shown in association with the penton base
protein. (B) The modeled proximal domain is rotated ~90 degrees with
respect to the view in panel A to show the interaction with a single
penton base protrusion. (C) The same view as in panel B but with the
protrusion removed to reveal the RGD-binding cleft on the inner
surface. The scale bars are 25 Å.
|
|
 |
DISCUSSION |
Comparison of integrin binding to Ad2 and Ad12.
We report the
structure of Ad2 and Ad12 complexed with its internalization receptor,
v
5 integrin. Detailed structural and functional
analyses of integrin have been hindered by the inherent difficulties in
isolating and purifying
v integrins from human tissue,
as well as in generating amounts large enough for structural analysis.
Recent expression of the ectodomain of integrin
v
5 as
a soluble recombinant protein (34) has allowed us to
characterize the structural interactions of
v
5
integrin with human Ads by cryo-EM image reconstruction. Previous
studies have shown that the Ad2 penton base protrusion, like several
native RGD ligands, binds integrin via a highly flexible RGD loop
(4, 17, 43). We reasoned that the flexibility of the Ad2 RGD
loop would not sufficiently constrain the position of the bound
integrin to allow structural characterization. Thus, we also chose to
examine another Ad serotype (Ad12) with a much shorter variable RGD
flanking sequence, as it has been reported that virus cell entry by
both Ad2 and Ad12 is mediated via
v integrins
(7). We hypothesized that a more rigid, well-defined
integrin structure would be observed for the Ad12 complex.
Consistent with this hypothesis, the structures of Ad12-integrin and
Ad2-integrin, solved in parallel and scaled equivalently,
reveal the
integrin density in the Ad12 complex to be compact
and well defined,
whereas that in the Ad2 complex is weak and
diffuse. Differences in
receptor occupancy are unlikely to account
for the more diffuse
integrin density of the Ad2 complex, as soluble
v
5
has been shown by solid-phase binding assays to have a higher
binding
capacity for Ad2 than for Ad12 (
34). Moreover, integrated
density measurements on the cryo-EM structures indicate that there
is
actually an ~30% greater occupancy of the integrin receptor
on Ad2
than on Ad12. We also noted that the penton base protrusion
in the
uncomplexed Ad2 has more weak, diffuse density than the
Ad12
protrusion. Taken together, these observations indicate that
the
v
5 integrin in the Ad2 complex is bound via a highly
flexible
RGD surface loop and hence does not have a well-constrained
orientation.
This explains the observation of diffuse, disconnected
integrin
density for the Ad2 complex and the measurement of an apparent
integrin volume that is 150% of that expected. In contrast, the
v
5 integrin is rigidly bound to the smaller, less
mobile Ad12
RGD protrusion, making a detailed structural analysis
possible.
Although the total height of the soluble integrin was the same for both
reconstructions (145 Å), the integrin in the Ad2 complex
was located
farther from the surface of the viral capsid. This
suggests that the
Ad2 loop is more extended than the Ad12 loop.
A more extended and
flexible RGD loop may facilitate
v
5 integrin
binding,
accounting for both the higher measured binding capacity
of the Ad2
penton base for
v
5 and the higher integrin occupancy
in the Ad2
complex.
Integrin structural features.
The cryo-EM reconstruction of
soluble recombinant
v
5 integrin bound to Ad12 reveals
a ring-like integrin structure above the penton base protein. The
integrin is observed to consist of two discrete domains, a globular
proximal domain and a flexible, tail-like distal domain (Fig.
8). The visualization of a two-domain structure is in agreement with that seen previously by rotary-shadow, negative-stain, and freeze-fracture EM. The cryo-EM integrin density extracted in Fig. 7C, which is estimated to correspond to a proximal domain from one
v
5 heterodimer, has dimensions of 65 Å in depth, 80 Å in height, and 90 Å in width (between the estimated
boundaries). Previous measurements of 80 by 80 Å (41), 80 by 100 Å (12), and 80 by 120 Å (37, 48) are in
rough agreement with the cryo-EM dimensions. The reconstructed integrin
density presented here also reveals an ~20-Å-diameter RGD-binding
cleft on the inner surface of the integrin proximal domain, a
structural feature not previously observed. Most integrin-binding RGD
motifs have been found on extended surface loops (2, 28, 29)
and would likely fit within a cleft of this size.

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FIG. 8.
Schematic diagram of the soluble v 5
integrin heterodimer. Approximate dimensions are derived from the
cryo-EM reconstruction of the Ad12-integrin complex. Amino acid residue
numbers are from Mathias et al. (34). The proximal and
distal domains are defined with respect to the viral surface.
|
|
Comparison of integrin and antibody binding to the Ad RGD
loop.
Surface plasmon resonance was used to measure antibody and
integrin associations with Ad particles in real time. We sought to
minimize steric hindrance as well as alteration of the native virus
structure during the immobilization step by indirectly linking Ad2
particles to a biosensor chip via a MAb directed against the distal
domain of the elongated fiber protein. Under these conditions, ~4.2
integrins but only ~1.7 antibody molecules were found to bind on
average to each penton base protein in the intact virus particle. The
stoichiometry of antibody binding to purified penton base protein was
previously reported to be ~2.8 (43). The lower value
obtained for intact virus particles might be due to steric hindrance
from the fiber protein. In the present study, we also report that the
apparent affinity of integrin was markedly lower than that of the DAV-1
antibody for the penton base. The measured affinity of
v
5 integrin obtained in the BIAcore studies
(KD = 73 nM) is very close to that previously
determined in Scatchard analyses of soluble penton base binding to
cells (KD = 55 nM) (49). The slower
on-rate (ka) for integrin versus antibody
molecules may be due to a number of factors, including their larger
mass and the possibility that the number of ligand-binding sites
becomes limiting as more integrin molecules are bound over time.
Mass considerations alone would suggest that fewer molecules of
v
5 integrin (250 kDa) would bind to penton base
relative
to DAV-1 MAb (150 kDa). However, the linear, two-domain shape
of the integrin, unlike the Y-shape of the immunoglobulin G antibody,
appears to be more conducive for binding to the closely spaced
penton
base protrusions (~60 Å apart). In addition, intermolecular
associations between bound integrin molecules, but not antibodies,
may
promote full occupancy on the penton base
protein.
Implications for Ad-induced integrin complex formation.
In the
Ad12-integrin reconstruction, the bound integrin molecules were
observed to form a continuous ring, exhibiting close contact between
neighboring receptors. The interactions between adjacent receptors are
likely to constrain the position and orientation of the individual
integrin heterodimers. In the case of Ad2, the more diffuse integrin
density observed in the complex may arise from the integrin ring moving
as a single unit of five interlocked heterodimers. As the Ad12 RGD
protrusion is less flexible, the bound integrin ring in the Ad12
complex has a more constrained position and hence better-defined
density. Since integrin-mediated signaling pathways are activated in
response to receptor occupancy and/or clustering, the
v
5 ring structure visualized by cryo-EM may represent
a conformation capable of inducing signals involved in virus
endocytosis (31, 32). In support of this idea, the Ad penton
base, but not a monomeric RGD peptide derived from the penton base,
activates p72 Syk kinase and also promotes adhesion of B lymphoblastoid
cells (45). These structural and biochemical findings are
consistent with the possibility that integrin clustering in the plane
of the cell membrane following interaction with multivalent ligands
plays a role in facilitating signaling events.
Receptor redistribution and clustering at adhesion sites play crucial
roles in signal transduction events mediated by integrins.
In vitro
binding experiments have shown that integrin occupancy
and integrin
aggregation can each mediate separate biological
signaling events
(
36). The synergistic action of both stimuli
was required to
induce the accumulation of cytoskeletal proteins
that mediate cell
adhesion. In addition, adhesion-dependent apoptosis
and cell spreading
by integrins were found to be stimulated by
multimeric rather than
monomeric ligands (
14). These studies
also suggest that
transmembrane signaling by integrin not only
occurs as a result of
receptor clustering following ligand binding
but is also dependent on
the precise spatial arrangement of the
bound receptor molecules. Our
structural results with the Ad-integrin
complex suggest that such
integrin clustering may occur via interactions
between the globular,
RGD-binding
domains.
During the course of evolution, various signaling pathways have been
exploited by viruses and other pathogens to gain entry
into host cells
(
19). The icosahedral structure of many viruses,
with two-,
three-, and fivefold axes, readily enables the mimicking
of native
multimeric ligands. Interestingly, the spacing of the
integrin-binding
RGD sites on Ad, ~60 Å, is virtually identical
to that on
foot-and-mouth disease virus, which is evolutionarily
unrelated
(
1,
26). The fivefold symmetry of the Ad penton
base
promotes the formation of an integrin ring structure that
may play a
key role in mediating virus internalization. It is
possible that
integrin interactions with their natural ligands,
extracellular matrix
proteins, also involves direct associations
between receptor
ectodomains, allowing regulation of integrin-mediated
cell
functions.
 |
ACKNOWLEDGMENTS |
We express our gratitude to Mike Galleno (Invitrogen) for helpful
suggestions on the expression of soluble
v
5. We also
thank Jack Johnson for reading the manuscript and David Cheresh and members of his laboratory for helpful comments.
This work was supported by NIH grants HL54352 and EY11431 to G.R.N. and
AI42929 to P.L.S. C.Y.C. was supported by a fellowship from the
Life and Health Insurance Medical Research Fund, a NIH-MSTP training
grant (GM08042), and the Aesculapians fund of the UCLA School of Medicine.
 |
FOOTNOTES |
*
Corresponding author. Mailing address for Phoebe L. Stewart: Department of Molecular and Medical Pharmacology, UCLA School of Medicine, A-324 CIBI, Box 951770, Los Angeles, CA 90095-1770. Phone:
(310) 206-7055. Fax: (310) 206-8975. E-mail:
pstewart{at}mednet.ucla.edu. Mailing address for Glen R. Nemerow: Department of Immunology, The Scripps Research Institute, La
Jolla, CA 92037. Phone: (619) 784-8072. Fax: (619) 784-8472. E-mail:
gnemerow{at}scripps.edu.
 |
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Journal of Virology, August 1999, p. 6759-6768, Vol. 73, No. 8
0022-538X/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
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