Cryo-electron microscopy structure of the SADS-CoV spike glycoprotein provides insights into an evolution of unique coronavirus spike proteins

Hongxin Guan; Youwang Wang; Abdullah F.U.H. Saeed; Jinyu Li; Syed Sajid Jan; Vanja Perculija; Yu Li; Ping Zhu; Songying Ouyang

R) . Unlike the other CTDs of (Fig. 2N-R) . of CTDs as its receptor binding motif (RBM). As a result, we propose that 275 SADS-CoV also uses these loops on the CTD as its RBM (Fig. 2N-P) . The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.976258 doi: bioRxiv preprint CoVs CTDs the downstream structure, but the evolutionary direction could go 287 either way [21] . Hence, we propose that the SADS-CoV S1-CTD located 288 between the other α -, δ -CoVs, and β -CoVs CTDs on the evolutionary 289 spectrum (Fig. 2N-R) . The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.976258 doi: bioRxiv preprint CoV, MERS-CoV, HKU1 and OC43 (Table S2) . Taken together, these results 339 are consistent with that of the sequence alignment. Fig. 3B-3D ) and the CTDs of SARS-CoV-2, SARS-CoV 353 and SADS-CoV (Fig. 3E) . Surprisingly, although SARS-CoV-2, SARS-CoV 354 and SADS-CoV CTD do not share significant sequence homology and belong 355 to a different family of CoVs (Fig. 3A) , they share roughly identical 356 organization and core folding (Fig. 3E) . Notably, SADS-CoV uses the variant On the one hand, the SADS-CoV S has a classical compact structure as 383 other α -CoVs, which uses the intra-subunit packing mode ( Fig. 2A-2B) . As a 384 result, this kind of architecture can maximally reduce the surface area of the S 385 protein to the immune system. Moreover, all of the NTDs and CTDs in a "lay 386 down" station (closed conformation) can further reduce immune pressure 387 (Fig. 2F) . Nevertheless, the NTDs and CTDs still have the chance to expose 388 for receptor binding. Furthermore, they can also be selected as single-or two- They are mainly located on the surface of S1 rather than on S2 like HCoV-401 NL63 (Fig. 4A) . In contrast to that, HCoV-NL63 S evades host immune 402 surveillance mainly by glycan shielding its S2 epitopes, SADS-CoV spike 403 appears to evade host immune surveillance mainly by glycan shielding its S1 linked glycosylation sites are located on the CTD (Fig. 4A-4B) . As a result, The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.976258 doi: bioRxiv preprint 669 S1-NTD, S1-CTD, SD1 and SD2 are colored by cyan, green, gray and red, 670 respectively. In the native state, only interactions between S1-CTD and S1-671 NTD of neighbor monomer are visible in SARS-CoV S (dotted circle in panel 672 A). S1-CTD is dissociated from S1-trimer when binding ACE2 in the prefusion 673 state. While in SADS-CoV spike, three interaction regions are visible in the 674 native state (dotted circles in panel B), including S1-CTD and S1-NTD of 675 neighbor monomer, internal S1-CTD and S1-NTD, S1-CTD trimer. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.976258 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.976258 doi: bioRxiv preprint