Three-dimensional structure of poliovirus receptor bound to poliovirus

Abstract

Poliovirus initiates infection by binding to its cellular receptor (Pvr). We have studied this interaction by using cryoelectron microscopy to determine the structure, at 21-A resolution, of poliovirus complexed with a soluble form of its receptor (sPvr). This density map aided construction of a homology-based model of sPvr and, in conjunction with the known crystal structure of the virus, allowed delineation of the binding site. The virion does not change significantly in structure on binding sPvr in short incubations at 4 degrees C. We infer that the binding configuration visualized represents the initial interaction that is followed by structural changes in the virion as infection proceeds. sPvr is segmented into three well-defined Ig-like domains. The two domains closest to the virion (domains 1 and 2) are aligned and rigidly connected, whereas domain 3 diverges at an angle of approximately 60 degrees. Two nodules of density on domain 2 are identified as glycosylation sites. Domain 1 penetrates the "canyon" that surrounds the 5-fold protrusion on the capsid surface, and its binding site involves all three major capsid proteins. The inferred pattern of virus-sPvr interactions accounts for most mutations that affect the binding of Pvr to poliovirus.

Figure 1

(a) Cryomicrographs of poliovirus particles complexed with (Top) and without (Bottom) sPvr. Bar = 300 Å. Image reconstructions are shown of virion + sPvr [in stereo (b)] and, for comparison, of the virion (c) (from ref. 9). The two reconstructions were overlaid in d with the respective contour levels adjusted to clarify the interaction of sPvr with the virion. Bar = 100 Å. (e) Two views of a single sPvr molecule extracted from the difference map. Domain boundaries are marked. Bar = 25 Å.

Figure 2

(a) A central section through the virion–sPvr reconstruction, normal to a 2-fold symmetry axis. The boxed region is shown in b. High density is shown as dark. The right edge of the box coincides with a 5-fold symmetry axis. (b) The virion–sPvr (Top) and virion (Bottom, from ref. 9) maps were oriented as in a rotated progressively about the 5-fold symmetry axis. (Left to Right) The rotation is −18°, 0°, 6°, 12°, 24°, and 30°. In each case, the boxed portion of the central section was extracted. Arrows indicate sPvr-related density that bridges the canyon (second panel from right) and the solvent-level density corresponding to the tunnel (rightmost panel). Bars = 50 Å.

Figure 3

(a) “Road map” representations (36, 37) of poliovirus (Left) and rhinovirus-14 [Right; (33)]. The corresponding triangular area of the capsid surface, bounded by a 5-fold and two 3-fold icosahedral symmetry axes, is marked (Inset). The radial distances of surface residues from the virion center are color coded and contoured [see key (Top Right)]. Nomenclature: 3145, residue 145 of VP3. The receptor footprints are shown in white. (b) A ribbon diagram (38) of the sPvr model is flanked by two views (39) of a single sPvr molecule as portrayed in the cryoelectron microscopy density map (white cage), enclosing the model of the three sPvr domains, d1 (cyan), d2 (orange), and d3 (violet). Carbohydrates attached to d2 [to N188 (Left) and N237 (Right)] and possibly to d1 are shown in brown. Also shown are the capsid proteins VP1 (blue), VP2 (yellow), VP3 (red), and VP4 (green). The tunnel beneath the sPvr-binding site is evident (white arrows). “Pocket factor” is magenta. (c) The sPvr sequence is mapped onto secondary structural elements of the homology model. Asn residues thought to be glycosylated are marked with asterisks. (d) Ribbon diagram (38) showing the docking of the sPvr model onto the capsid surface. Same color conventions as in b. The axes allow this view to be related to Fig. 4. (e) Schematic diagram showing a possible binding configuration of poliovirus with intact membrane-bound Pvr.

Figure 4

Ribbon diagram (38) of the capsid-binding d1 domain of Pvr (cyan), with β-strands labeled, juxtaposed with segments of the capsid proteins with which it is inferred to interact. The viral segments are shown as tubes, with VP1, blue; VP2, yellow; and VP3, red. Residue numbers are provided as landmarks. Black balls and colored numbers denote amino acids implicated by genetic analysis in receptor binding. Similarly, Pvr residues shown by mutation to be important for virus binding are listed (Left). The axes allow this view to be related to Fig. 3d.