2 files

Glycosylated Swiss-model molecular dynamics trajectory of SARS-CoV-2 spike glycoprotein

posted on 08.05.2020 by Oliver Grant, Robert Woods
Molecular dynamics simulation trajectory. The system is the SARS-CoV-2 spike glycoprotein with glycans modeled on using GLYCAM-Web. SARS-CoV2 spike (S) protein structure – A 3D structure of the prefusion form of the S protein (RefSeq: YP_009724390.1, UniProt: P0DTC2 SPIKE_SARS2), based on a Cryo-EM structure (PDB code 6VSB), was obtained from the SWISS-MODEL server (swissmodel.expasy.org). The model has 95% coverage (residues 27 to 1146) of the S protein.
The site specific glycans used to model a glycoform representative of the data obtained from the S glycoprotein expressed in HEK293 cells, are presented below: Hybrid: DManpα1-6[DManpα1-3]DManpα1-6[DGlcpNAcβ1-2DManpα1-3]DManpβ1-4DGlcpNAcβ1-4DGlcpNAcβ1-OH Glycosites: 657 FA2: DGlcpNAcβ1-2DManpα1-6[DGlcpNAcβ1-2DManpα1-3]DManpβ1-4DGlcpNAcβ1-4[LFucpα1-6]DGlcpNAcβ1-OH Glycosites: 149, 165, 331, 343, 616, 1134 A2: DGlcpNAcβ1-2DManpα1-6[DGlcpNAcβ1-2DManpα1-3]DManpβ1-4DGlcpNAcβ1-4DGlcpNAcβ1-OH Glycosites: 1098 FA2B: DGlcpNAcβ1-2DManpα1-6[DGlcpNAcβ1-4][DGlcpNAcβ1-2DManpα1-3]DManpβ1-4DGlcpNAcβ1-4[LFucpα1-6]DGlcpNAcβ1-OH Glycosites: 74, 282 M5: DManpα1-6[DManpα1-3]DManpα1-6[DManpα1-3]DManpβ1-4DGlcpNAcβ1-4DGlcpNAcβ1-OH Glycosites: 61, 122, 603, 709, 717, 801, 1074 M8: DManpα1-2DManpα1-6[DManpα1-2DManpα1-3]DManpα1-6[DManpα1-2DManpα1-3]DManpβ1-4DGlcpNAcβ1-4DGlcpNAcβ1-OH Glycosites: 234 Glycan naming system. In cases where the mass spectrometry data allows for multiple structures, such as FA2/FA1B, the glycan with the least ambiguity was selected. For example, FA2 was selected over FA1B, as the position of the single antennae is ambiguous.

Dataset supports the following preprint: 3D Models of glycosylated SARS-CoV-2 spike protein suggest challenges and opportunities for vaccine development. Oliver C. Grant, David Montgomery, Keigo Ito, Robert J. Woods; bioRxiv 2020.04.07.030445; doi: https://doi.org/10.1101/2020.04.07.030445


Tools to enable non-specialists to model glycoconjugates and glycan-protein interactions

National Cancer Institute

Find out more...

Resource for Integrated Glycotechnology

National Institute of General Medical Sciences

Find out more...

National Institute of Allergy and Infectious Diseases (NIAID)

United States Department of Health and Human Services

Find out more...


Select an IC:

  • AI - National Institute of Allergy and Infectious Diseases (NIAID)
  • CA - National Cancer Institute (NCI)
  • GM - National Institute of General Medical Sciences (NIGMS)

Is this associated with a publication?


I confirm there is no human identifiable information in this dataset.