Supramolecular architecture of severe acute respiratory syndrome coronavirus revealed by electron cryomicroscopy

Abstract

Coronavirus particles are enveloped and pleomorphic and are thus refractory to crystallization and symmetry-assisted reconstruction. A novel methodology of single-particle image analysis was applied to selected virus features to obtain a detailed model of the oligomeric state and spatial relationships among viral structural proteins. Two-dimensional images of the S, M, and N structural proteins of severe acute respiratory syndrome coronavirus and two other coronaviruses were refined to a resolution of approximately 4 nm. Proteins near the viral membrane were arranged in overlapping lattices surrounding a disordered core. Trimeric glycoprotein spikes were in register with four underlying ribonucleoprotein densities. However, the spikes were dispensable for ribonucleoprotein lattice formation. The ribonucleoprotein particles displayed coiled shapes when released from the viral membrane. Our results contribute to the understanding of the assembly pathway used by coronaviruses and other pleomorphic viruses and provide the first detailed view of coronavirus ultrastructure.

FIG. 1.

Cryo-EM of coronaviruses in vitreous ice. SARS-CoV-Tor2 (A and B), FCoV-Black (C), MHV-OBLV60 (D), and tunicamycin-grown MHV-OBLV60 (E) are shown in “reversed” contrast, with density in white. Images were recorded at ∼2.5 microns below true focus (B, C, right-hand portion of panel D, and E), ∼4.0 microns under focus (A), and ∼20 microns under focus (left-hand portion of panel D). The scale bar represents 100 nm.

FIG. 2.

Cryo-EM of pleomorphic SARS-CoV virions. Shown is a gallery of images at −2 to −4 microns defocus to illustrate surface and interior topography. The scale bar represents 100 nm.

FIG. 3.

Disposition of densities in the membrane-proximal region. (A) Rotationally averaged radial density profiles were generated for 30° wedges taken from intact coronavirus particles. Wedges from SARS-CoV (n = 80), FCoV (n = 41), MHV (n = 53), and TUN-MHV (n = 82) particles were aligned on the minimum-density node between the headgroup densities of the lipid bilayer. The schematic above interprets densities in the spike protein (S), membrane-proximal and matrix protein (M), and ribonucleoprotein (RNP) regions. Entire SARS-CoV virions and adjacent regions of background vitrified ice, recorded at two levels of focus, are presented as reciprocal space power spectra (B). Prominent features are noted at ∼15 nm⁻¹ (heavy red bracket) and ∼5 to 8 nm⁻¹ (dotted bracket). An averaged power spectrum for ∼1,000 aligned SARS-CoV edge views (C) or the extraviral (outer) or interior (inner) portion of the image is also shown. The scale bar represents 10 nm. Prominent features are marked as described for panel B. Edge views (C, entire) were divided into upper (D, outer), membrane-proximal (D, middle), or lower (D, inner) thirds. The correlation coefficient was calculated for a static copy of each image and another copy of the same image that was shifted in 1-pixel increments. Peaks of correlation are marked as described for panel B.

FIG. 4.

Analysis of viral features in axial views. (A) Axial spike images were selected from the central region of each virion (left image) and masked around one spike (center and right images). (B) An averaged image from unaligned, unmasked, manually centered SARS-CoV axial views is also shown. (C) Axial images of SARS-CoV (column 1), FCoV (column 2), MHV (column 3), and TUN-MHV (column 4) were aligned and averaged iteratively until a stable averaged image emerged (row b). Axial images were filtered in Fourier space to remove image data greater than (row a) or less than (row c) 9 nm. Filtered axial images were averaged, the averaged image was refined by 10 rounds of iterative alignment and averaging, and then unfiltered images were aligned to the averaged filtered image for a further two cycles to produce the images shown (rows a and c). Insets show Fourier transforms of the corresponding averaged images. (D) One virion that displayed reflections corresponding to the spike and RNP lattices is shown, together with a Fourier transform of the core region (inset). The scale bar represents 10 nm.

FIG. 5.

Analysis of SARS-CoV paracrystalline lattices. The SARS-CoV RNP lattice (Fig. 4C, column 1, row a) was used as the starting image for 10 cycles of alignment and averaging (A, left image). Reflections were selected from the Fourier transform of this image (A, right) and back transformed to reveal the overlapping RNP (B, left) and spike (B, right) lattices. (C) Lattices similarly obtained from reflections in Fourier transformed FCoV (left) and MHV images (right) show similar RNP organization. (D) The two lattices are shown superimposed and averaged (left) and in schematic form (right). (E) A reference-free class average of axial SARS-CoV images recorded slightly farther from focus shows triangular spikes (left), also seen in the example principal component eigenimage (center) and in reconstructed images (right). (F) An example eigenimage from TUN-MHV, showing only RNP densities, is presented for comparison. The scale bar represents 10 nm.

FIG. 6.

Analysis of the structural proteins as seen in edge views. (A) Boxed images were centered on the viral membrane below one spike, as shown in the averaged image of aligned SARS-CoV edge views. (B) A keystone-shaped mask (shown in panel A) was applied to individual edge views before reference-free classification and averaging. (C) Edge-view class averages show the ultrastructure of the membrane-associated structural protein complex. Class averages of FCoV (D), MHV (E), and spike-depleted TUN-MHV (F) were obtained by the same process. Intramembrane densities ascribed to viral M protein are indicated with black arrowheads in SARS-CoV (G) and TUN-MHV (H). Connecting densities between the RNP and membrane regions are indicated with small white arrowheads. (I) A spontaneously disrupted SARS-CoV particle shows RNP strands escaping from a spherical core, recorded at −4 μm (left) and −2.4 μm (right) under focus. The narrowest parts of the RNP are indicated with white arrowheads, and the membrane section remaining with the core is indicated with large black arrowheads (left). The bilayer densities are more visible in the near-focus image, indicated with small black arrowheads (right). The scale bars represent 10 nm.

FIG. 7.

Interpretation of coronavirus virion structure. Conserved structural proteins are drawn as they appear in edge views (left) and axial views (right). Trimeric spikes (S) are shaded in red, membrane proteins (M) are in solid blue, and nucleoproteins (N) are shaded in violet. The dimensions of lattices of S trimers (a = 14.0 nm, b = 15.0 nm, γ = 100°) and RNP molecules (c = 6.0 nm, d = 7.5 nm, ɛ = 100°) were determined from the reflections shown in Fig. 5A and were consistent with real-space measurements of the same parameters.