PDB files of SARS-CoV-2 Spike Protein Glycoforms

Here we have generated 3D structures of glycoforms of the spike (S) protein SARS-CoV-2, based on reported 3D structures for the S protein and on reported glycomics data for the protein produced in HEK293 cells. We also report structures for glycoforms that represent those present in the nascent glycoproteins (prior to enzymatic modifications in the Golgi and ER), as well as those that are commonly observed on antigens present in other viruses. These models were subjected to MD simulation to take into account protein and glycan plasticity, and to determine the extent to which glycan microheterogeneity impacts antigenicity. Lastly, we have identified peptides in the S protein that are likely to be presented in human leukocyte antigen (HLA) complexes, and discuss the role of S protein glycosylation in potentially modulating the adaptive immune response to the SARS-CoV-2 virus or to a related vaccine.本研究基于已发表的严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）刺突（S）蛋白三维结构，以及HEK293细胞表达该蛋白所得的糖组学数据，构建了该病毒刺突蛋白的多种糖型三维结构。同时，本研究还报道了两类糖型的结构：一类对应尚未经历高尔基体（Golgi）与内质网（ER）中酶促修饰的新生糖蛋白所含的糖型，另一类则是其他病毒抗原上常见的糖型。为了探究蛋白质与聚糖的构象可塑性，并明确聚糖微异质性对抗原性的影响程度，我们对上述模型开展了分子动力学（MD）模拟。此外，本研究还鉴定出了可能被人类白细胞抗原（HLA）复合物呈递的S蛋白肽段，并讨论了S蛋白糖基化在调节SARS-CoV-2病毒或相关疫苗的适应性免疫应答中所发挥的潜在作用。