Characterization of the SARS-CoV-2 Spike in an Early Prefusion Conformation

Tingting Li; Qingbing Zheng; Hai Yu; Dinghui Wu; Wenhui Xue; Yuyun Zhang; Xiaofen Huang; Lizhi Zhou; Zhigang Zhang; Zhenghui Zha; Tingting Chen; Zhiping Wang; Jie Chen; Hui Sun; Tingting Deng; Yingbin Wang; Yixin Chen; Qinjian Zhao; Jun Zhang; Ying Gu; Shaowei Li; Ningshao Xia

The mutant included two stabilizing proline mutations at residues 986, 987 and a 218 "GSAS" substitution at the furin cleavage site 7 . Surprisingly, the alignment 219 demonstrated that the two cryo-EM structures share similar mushroom-shaped 220 architecture in particular nearly identical at stalk moiety (S2 region), but our S-pre 221 shows the cap part (S1 region) at ~15Ã… lower position than the reported S trimer in 222 RBD-down prefusion conformation (Fig. 4D ). Regarding to substantial mismatch at the 223 density of 3 S1 subunits, we respectively fitted 5 individual domains (NTD, RBD, SD1, 224 SD2 and S2) of the SARS-CoV-2 S structure (PDB code 6VSB) to our S-pre map. In 225 the fitting map, NTD, RBD, SD2 and S2 could be well placed in the S-pre map, 226 especially for the latter two, which reflects the aforementioned good match at the stalk 227 of the mushroom-shape ( Supplementary Fig. 2) . However, there is no observable 228 density between RBD and SD2 to accommodate an SD1 model ( Supplementary Fig. 2 CoV-2 spike may retain at more precedent state than the classic prefusion conformation 294 that has been determined for other coronaviruses. This early prefusion conformation 295 features that the cap of the mushroom-shaped spike constituted by three S1 subunits is 296 more proximal to viral membrane by 15 Ã… than in the classic prefusion conformation.