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Journal of Virology, June 2003, p. 6101-6107, Vol. 77, No. 11
0022-538X/03/$08.00+0 DOI: 10.1128/JVI.77.11.6101-6107.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
and R. Holland Cheng
Department of Biosciences, Karolinska Institute, 141 57 Huddinge, Sweden
Received 31 October 2002/ Accepted 3 March 2003
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The most highly conserved structural feature among HRVs is a surface depression around the fivefold axes, the so-called canyon (25). The canyon is composed of the north wall (built by VP1) around the fivefold axis and the south wall (built mainly by VP2 and VP3). While the most accessible residues along the canyon walls are hypervariable, the less exposed residues in the canyon floor are conserved and used for receptor binding, as the strategy allowing the virus to escape antibody neutralization (23). There is a hydrophobic pocket in VP1 directly underneath the canyon floor. The pocket appears empty in HRV3 and HRV14 (29) but is filled with electron density resembling a fatty acid (pocket factor) in the structures of HRV2 and HRV16 (10, 27). The pocket factor stabilizes the virion during its cell-to-cell transit (19). Hydrophobic antiviral compounds (WIN compounds) were found to bind to the VP1 pocket and to inhibit capsid breathing (17).
The major group of HRVs use the canyon region for binding to its cellular receptor, intercellular adhesion molecule 1 (ICAM-1) (16). ICAM-1 is a membrane protein with five immunoglobulin-like domains in the extracellular region. The critical virus binding epitopes are present at the tip of the N-terminal first domain (D1) of ICAM-1 (16), which penetrates into the rhinovirus depressive canyon (2, 16). The low accessibility of the receptor binding site in the major group of HRVs correlates with a low virus-receptor association rate (28). Binding of ICAM-1 to HRV3 and HRV14 (receptor-sensitive serotypes) triggers the release of the RNA genome from the capsid (uncoating), but this does not occur with other members of the major group of HRVs (13, 28). Receptor-mediated uncoating has been reported for the major group of HRV and poliovirus, showing that these viruses use their receptors for both virus attachment and uncoating (13, 15, 21). Indeed, entry of poliovirus and receptor-sensitive rhinoviruses (HRV14) can occur without endosomal acidification (20, 26).
The structural changes mediated by the receptor in the virus particles lead to the release of the RNA genome from the capsid for penetration into the cell cytoplasm (13, 15, 21). It has also been proposed that the RNA will move through a membrane pore generated by the externalized N-terminal region of VP1 and VP4 during the uncoating process (3). Externalization of those polypeptides has been supported by two structural analyses of high-temperature (>50°C)-treated poliovirus and a minor-group rhinovirus, which have provided new insights into picornavirus uncoating (3, 12). However, no structural analysis of receptor-mediated uncoating has been reported so far, in contrast to the well-documented biochemistry of this process (5, 13, 15). The precise mechanism by which a cellular receptor triggers the exit of the viral genome is currently unknown. To gain new insight into this process, we applied cryoelectron microscopy (cryo-EM) to a well-defined model, HRV3 and its ICAM-1 receptor (5, 13). Our results indicate that the receptor catalyzes uncoating by locking the viral capsid in an expanded open state for subsequent RNA release.
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Structure determination and analysis. A Philips CM120 microscope equipped with a Gatan cryotransfer system was used to photograph the HRV-receptor complex. The micrograph then was digitized at 3.1 Å/pixel on a SCAI scanner. Images of individual particles were boxed out for further analysis based on icosahedral symmetry (7). The data from the large defocus film was processed first to get a stable model map for the close-defocus data. The H3RC complex was reconstructed to a resolution of 23 Å by combining 125 individual close-defocus images. The H3RC reconstruction served as the initial model to assign the center and the orientation of the particles at 37°C (H3RH and H3Re). The single-image reconstructions were used to aid the particle selection and to help in fine-tuning the intermediate polar Fourier transform models (1). The size of individually boxed H3RH images was determined by correlating the observed data with the corresponding projection of the H3RC reference map by grid interpolation. The Gaussian distribution of the particle size of H3RH versus H3RC was shifted, with a 4% increase in the mean value. The final reconstruction of H3RH and H3Re complexes was resolved to 23 and 25 Å by using 91 and 64 particles, respectively. The resolution was determined by R-factor assessment. The completeness of the data sampling in the reconstruction was verified by obtaining eigenvalue spectra, showing that of eigenvalues were >1 or 10 (8).
In a particular experiment, the internal size standard was generated by the addition of a large portion of native HRV3 particles to the 37°C-treated HRV3-receptor mixture after it was chilled on ice. The empty HRV3-receptor complex and full particles, mainly including unheated HRV3, were boxed out from a single micrograph and were used to calculate three-dimensional maps. Comparison of these three-dimensional reconstructions gave 4% size difference. The consistent dimensions of the bound ICAM-1 molecule (
75 Å long and
20 Å in diameter) in the three complexes demonstrated no detectable systematic error due to the microscope. Finally, the consistent size of the HRV16-receptor complexes at different temperatures was an additional control for the collection of low-dose imaging of microscope data.
Model fitting. Fitting of the ICAM-1 receptor (PDB access number 1IC1) and the HRV3 crystal structures (PDB access number 1RHI) into the cryo-EM density was performed manually using the program O (14). The docking of coordinates was done based on both visual and quantitative criteria. The HRV3 coordinates and H3RC map had the same origin. Domain 2 of the ICAM-1 molecule first was fitted into the corresponding EM density, with a previously described orientation as reference (16). The position of receptor domain 1 was adjusted manually. To model the capsid movement in the H3RH structure, the alpha-carbon coordinates of ICAM-1 were fitted into the receptor density of the expanded particle and then the coordinates of the viral proteins were fitted individually into the H3RH map. VP2 and VP3 were moved out radially and tilted to best follow the density distribution. Based on the modeled ICAM-1 position with its unique density profile, contact between VP2 and ICAM-1 was maintained and was used to localize the position of VP2. Subsequently, VP1 was docked into the EM density before the position of the whole protomer was adjusted by minimizing the crash with neighboring protomers. The resulting model was used to calculate a set of structure factors from which an electron density map was generated at a resolution corresponding to the EM density. The real-space correlation between the calculated and experimental densities was computed, and the high value of the correlation coefficient in the H3RH fitting (0.79) indicated optimal positioning of the viral proteins. This value was similar to that of H3RC docking (0.80). The best correlation coefficient of H3Re fitting was 0.73 (data not shown).
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FIG. 1. Cryo-EM of HRV3-receptor complexes and uncoating intermediates. (A) Schematic view of the pathway of HRV3 uncoating mediated by soluble ICAM-1 binding (5) and the procedure used for preparation of virus-receptor complexes for cryo-EM. Arrows and hexagons represent the ICAM-1 receptor and the HRV particles, respectively. H3RC was prepared by incubation of HRV3 with ICAM-1 at 4°C, while H3RH and H3Re were prepared at 37°C as described in Materials and Methods. H3RC and H3RH preserve all viral proteins and RNA, while H3Re lacks both VP4 and RNA (5). (B) Micrograph of H3RC. (C) Micrograph of H3RH and H3Re complexes. About 40% of the particles appear empty (H3Re), lacking the internal RNA genome represented by a spiral line in panel A. Bar, 1,000 Å.
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-contoured map of H3Re. However, disappearance of the EM density of that ICAM-1 region in the H3RC and H3RH maps required contour levels of 3.5 and 3.8
, respectively. These data showed that the receptor molecule remained bound to the capsid during RNA release and suggest that the bound receptor slowly released from the capsid after the egress of RNA (5). The lower occupancy of ICAM-1 in H3Re could be also due to a less ordered bound receptor molecule.
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FIG. 2. Surface rendering of native HRV3 and virus-receptor complexes. The maps are viewed along the twofold axis and contoured at 1 above the average. The labels of the complexes correspond to the data acquisition scheme presented in Fig. 1. In the right column, maps truncated 10 Å below the surfaces at the fivefold axis are shown. The locations of icosahedral two-, three-, and fivefold axes are indicated by the numbers superimposed on the HRV3 reconstruction, which was computed from the crystallographic coordinates (29). Bar, 100 Å.
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FIG. 5. Virus-receptor binding surfaces. Side (top) and front (bottom) views of the fitted ICAM-1 and HRV3 crystal structures into the corresponding EM densities (grid) of the H3RC (A and D) and H3RH (B and E) complexes, superimposed in panels C and F. Density maps are contoured at 1.5 (top) and 2.0 (bottom) . A ribbon diagram of the two-domain crystal structure of ICAM-1 is shown, with the two interacting HRV3 protomers presented as worm drawings. The two connecting viral protomers are colored in yellow (left protomers in panels A, B, D, and E) and magenta (right protomers). In panels C and F, viral proteins VP1, VP2, and VP3 of H3RH are colored in blue, green, and red (the left protomer) or magenta (the right protomer), respectively; the superimposed H3RC protomer is colored in yellow. VP4 is cyan, and the N-terminal 60 residues of VP1 are gray. The red arrow points to the protruding density featuring the H3RH particle, predicted to be filled by the externalized VP4 and the VP1 N terminus. The side chain of the VP3 Tyr181 residue is indicated by purple spheres. The first (D1) and second (D2) domains of ICAM-1 are labeled, as are virus-binding BC, DE, and FG loops (6). The illustrations were prepared with the program PyMOL (http://www.pymol.org).
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FIG. 3. Size of the virus particles in the HRV-receptor complexes. Density profiles of the HRV reconstructions, presented as spherically averaged density versus particle radius, are shown. The arrows indicate the outer boundary of the viral capsid. (Top) Density distribution for the H3RC and H3RH reconstructions presented in Fig. 2. (Middle) Density distribution for HRV16-ICAM-1 complexes prepared at 4°C (H16RC) or 37°C (H16RH) as described in Materials and Methods. (Bottom) Density distribution for HRV3 native virions treated at 4°C (HRV3C) or 37°C (HRV3H) in the absence of receptor.
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FIG. 4. Capsid rearrangements in the HRV-receptor complexes. (A to C) Equatorial sections of H3RC (A), H3RH (B), and H3Re (C) reconstructions perpendicular to the icosahedral twofold axis. The icosahedral axes (two-, three-, and fivefold) are drawn on the section of H3RC. The contour plots circle the density distribution at 1 (blue) and 2 (red). The arrow in panel C indicates the twist movement predicted for VP1. (D) Top view of the H3RC and H3Re electron density maps of a viral pentamer. The H3Re density map (cyan grid lines) contoured at 2 is superimposed onto the H3RC isosurface map rendered at 3 . The red line indicates the location of the equatorial sections presented in panels A to C. An asterisk marks the canyon position. The illustrations were prepared with the NAG Explorer program.
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Receptor-virus binding contacts. The crystal structure of the two N-terminal domains of ICAM-1 fits well into the corresponding density of the H3RC and the H3RH maps (Fig. 5A and B). The receptor appears more bent in H3RH than in H3RC (Fig. 5C). The side of the first domain (ß-strands C and F) contacts the south wall of the canyon (the promoter is shown in yellow), and the tip (BC and FG loops of domain 1) penetrates into the canyon and sits on the junction of two closely associated promoters (Fig. 5D and E).
In H3RH, the neighboring promoters remain in contact at the fivefold axis region but are separated in the canyon (Fig. 5E); this is due mainly to the expansion of the capsid and to the slight movement of VP2 and VP3 toward the threefold axis (Fig. 5F). The docking of the viral proteins in H3RH is consistent with the preservation of the density organization at the fivefold axis as well as with the appearance of a density cleft at the canyon (Fig. 2 and 4) concomitant with capsid expansion. We have observed that residues such as Tyr181 of VP3 become exposed at the interprotomer junction of the fitted viral proteins in the expanded capsid. This residue could then interact with the critical Pro70 residue located in the FG loop of the receptor (Fig. 5B and E).
The internal N-terminal regions of VP1 and VP4 are located underneath the hole at the canyon region generated by capsid expansion. Those polypeptides then could externalize through this region and account for the protruding density connecting the receptor to the north wall of the canyon in H3RH (arrowhead in Fig. 5B and C). The externalized proteins may interact with the relatively hydrophobic DE loop of ICAM-1, which is involved in crystallographic dimeric association (6).
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FIG. 6. Dynamics of receptor-mediated rhinovirus uncoating. Schematic views of two neighboring protomers with a bound ICAM-1 receptor molecule, representing conformations of H3RC, H3RH, and H3Re complexes. Ovals, triangles, and pentagons indicate the positions of the twofold, threefold, and fivefold axes, respectively. VP1, VP2, and VP3 are represented as blocks colored blue, green, and red, respectively. Stable virus-receptor complexes (H3RC) are formed at low temperatures by receptor binding to a close virus conformation, represented by the crystal structure (28). The capsid dynamics (or breathing) opens the interprotomer junction, so that the internal N-terminal regions of VP1 and VP4 (labeled as N-VP1-VP4) became exposed simultaneously at physiological temperatures (17, 18, 22). This expanded conformation is maintained by receptor binding between two adjacent protomers and to the exposed region of VP1, as shown by the cryo-EM H3RH structure. Egress of the viral RNA genome and loss of VP4 result in major rearrangements in VP1 and the fivefold axis and subsequent release of the receptor from the H3Re complex.
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A protruding and well-defined density appeared, bridging the receptor and the north canyon wall in the expanded H3RH capsid, but it was absent in H3RC and H3Re (Fig. 2 and 5). This density might represent the externalized N-terminal regions of VP1 and VP4, which have been reported to exit simultaneously and reversibly from the capsid (17, 18). These polypeptides localize beneath the interprotomer interface in the native capsid (Fig. 5D). Thus, these two peptides may exit through the open canyon region and account for the protruding density featuring the H3RH intermediate. Externalization of these polypeptides through a similar location has been proposed for related picornaviruses (3, 12). Localization of the externalized polypeptides near the hydrophobic ICAM-1 dimerization region (6) suggests that they may interact with the receptor. This interaction could lock the VP1 N terminus and VP4 in their externalized conformations so that they could bind to the membrane (9).
The release of the RNA from the capsid of picornavirus is thought to occur through one of its 12-pentameric vertices. However, there has been no evidence showing the egress of the VP3 N-terminal cylinder connection, VP1 N terminus, VP4, or viral RNA through this opening. Analyses of uncoating intermediates in HRV3 presented here and in poliovirus (135S) (3) showed little evidence for the formation of a capacious tunnel through the fivefold axis region. Changes at the fivefold axis region arise after RNA egress and might lead to capsid disassembly (Fig. 2 and 4) (12).
While the fivefold axis regions of H3RC and H3RH particles are structurally similar, significant differences were observed along the interprotomer interfaces in the canyon region and at the twofold axis junctions (Fig. 2 and 4). These observations strongly suggest an expansive movement of the pentamers along the fivefold axis. Polarized expansion of a single receptor-attached, membrane-proximal pentamer could occur during virus entry. RNA egress through the expanded pentamer could then take place close to the membrane while the virus particle remains attached to the receptor, thereby facilitating penetration into the cell cytoplasm.
The results presented here reveal for the first time that capsid expansion can be mediated by receptor binding at physiological temperature. The magnitude of capsid expansion for the H3RH (4%) uncoating intermediate is similar to that observed for related picornavirus particles (3, 12), so that it must be significant for virus entry. We propose that the ICAM-1 receptor passively catalyzes uncoating by locking the capsid in an expanded and open intermediate state for subsequent RNA release (Fig. 6). In rhinovirus and related picornaviruses, this process can be attributed to the dynamic feature of the viral capsids (17, 18, 22), as well as the fragmented nature of the receptor binding site (4, 11, 16, 28). Expansion of nonenveloped virus capsids catalyzed by receptor binding or other cellular factors could precede uncoating during virus entry into cells, as shown here for HRV and its ICAM-1 receptor.
This work has been sponsored by grants from the Medical Research Council (MFR-12175 and MFR-12637) and the Natural Science Research Council (NFR-11691 and NFR-11994) to R.H.C. and J.M.C. L.X. is the recipient of a fellowship from the Swedish Structural Biology Network (to R.H.C.).
Present address for José M. Casasnovas: Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma, 28049 Madrid, Spain. Phone: 34 91 5854917. Fax: 34 91 5854506. E-mail: jcasanovas@cnb.uam.es. ![]()
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