The human coronavirus HCoV-229E S-protein structure and receptor binding
- The University of Toronto, Canada
- INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, Canada
- The Hospital for Sick Children Research Institute, Canada
Figures
Figure 1 with 1 supplement
Comparison of the RBD-hAPN complexes.
In all panels, the Class I RBD is colored magenta, the Class III, IV and V RBDs are colored cyan, and hAPN is colored gray. (a) Center: superimposition of the Class I, III IV and V RBD-hAPN …
Figure 1—figure supplement 1
RBD sequence Alignment.
The Class I RBD sequence corresponds to residues 293–435 of NCBI AAK32191.1. The Class II - VI RBDs possess the receptor binding loops and supporting residues of their respective RBD classes and the …
Figure 2 with 1 supplement
EM analysis of the HCoV-229E S-protein.
(a) An example negative stain micrograph. White arrowheads indicate particles with a readily discernable tail which is presumed to be formed by the HR2 region and the added foldon trimerization …
Figure 2—figure supplement 1
Orientation distribution of the 229E S-protein cryo-EM data.
In each panel, the 229E S-protein cryo-EM map is shown in the center. Left, side view; right, top view. Height and color of the columns indicate particle orientation frequencies.
Figure 3 with 1 supplement
Resolution of the HCoV-229E S-protein cryo-EM map.
(a) Local resolution (Å) plotted on the cryo-EM map surface as a heat map. Leftmost image, a side view of the map contoured at 3.0 RMS to show the weak densities of the connector domains (at …
Figure 3—figure supplement 1
Examples of the atomic model built into the 229E S-protein cryo-EM map.
(a–c) RBD segments containing the three receptor binding loops. The tip of Loop 1 showed weak density. (d) Residues 57–67 and the N-linked glycan at Asn62. (e) Residues 820–918, encompassing CH and …
Figure 4 with 1 supplement
Cryo-EM structure of the HCoV-229E S-protein.
(a) Domain structure of the S-protein. UH, upstream helix; HR1, heptad repeat 1; CH, central helix; CD, connector domain; HR2, heptad repeat 2. TM, transmembrane segment. Segments colored in white …
Figure 4—figure supplement 1
Fitting of the connector domain into its cryo-EM map density.
The cryo-EM map is contoured at 3.0 RMS to show the map density of the connector domain (blue ribbons).
Figure 5
Models of the complete HCoV-229E S-protein ectodomain and locations of the N-glycosylation sites.
(a) A composite model of the complete ectodomain showing the cryo-EM structure determined (enclosed by the box) and a homology model of the HR2 region based on PDB: 2FXP. For each N-glycan observed …
Figure 6
Key hydrophobic interactions defining the assembly of the HCoV-229E S-protein trimer.
(a) Hydrophobic interactions in the S1 region. Each monomer is colored white, gray and black, respectively. Apolar residues between the S1 subunits are colored cyan. (b) The S1 subunit of one …
Figure 7 with 1 supplement
The interfaces in the S2 helical core region of the HCoV-229E S-protein are hydrophilic.
(a,b) Bottom views of the interfaces in the S2 helical core region. For clarity only the three major components of the trimer interface in the S2 region are shown: UH, HR1821-871 and CH. The red …
Figure 7—figure supplement 1
The subunit interfaces in the helical core region are hydrophilic in coronaviruses.
For each coronavirus S-protein, the three interface-forming helices CH, UH and HR1 long helix are shown with all their apolar (green) or polar (cyan) residues. From left to right: bottom view, …
Figure 8
The HCoV-229E S-protein shows a large opening in the S2 region.
(a,b) Bottom views of the S-protein trimer at two contour levels showing the opening in S2 at (a) 1.5 RMS and (b) 3.0 RMS. The three S2 subunits are colored differently in (b). (c, d) Comparison of …
Videos
Video 1
Comparison of the 229E and NL63 S-proteins (Bottom view).
Two views showing a morphing between the two S-proteins. PDB ID: NL63, 5SZS. An S1 subunit is colored cyan. The S2 subunit with which it associates is from another monomer and it is colored blue.
Video 2
Comparison of the 229E and NL63 S-proteins(Side view).
Video 3
Comparison of the CH helix in the pre-fusion and post-fusion conformations of the MHV S-protein.
Top view showing the morphing between the two helices. PDB IDs: pre-fusion, 3JCL; post-fusion, 6B3O. Rotation of the CH helix during the conversion from the pre-fusion to the post-fusion …
Additional files
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Supplementary file 1
Cryo-EM data collection and refinement statistics.
- https://cdn.elifesciences.org/articles/51230/elife-51230-supp1-v2.docx
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Supplementary file 2
X-ray crystallographic data collection and refinement statistics.
**Values in parentheses are for the highest-resolution shell.
- https://cdn.elifesciences.org/articles/51230/elife-51230-supp2-v2.docx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/51230/elife-51230-transrepform-v2.docx
