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Structure paper

TitleIn situ architecture and membrane fusion of SARS-CoV-2 Delta variant.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 120, Issue 18, Page e2213332120, Year 2023
Publish dateMay 2, 2023
AuthorsYutong Song / Hangping Yao / Nanping Wu / Jialu Xu / Zheyuan Zhang / Cheng Peng / Shibo Li / Weizheng Kong / Yong Chen / Miaojin Zhu / Jiaqi Wang / Danrong Shi / Chongchong Zhao / Xiangyun Lu / Martín Echavarría Galindo / Sai Li /
PubMed AbstractAmong the current five Variants of Concern, infections caused by SARS-CoV-2 B.1.617.2 (Delta) variant are often associated with the greatest severity. Despite recent advances on the molecular basis ...Among the current five Variants of Concern, infections caused by SARS-CoV-2 B.1.617.2 (Delta) variant are often associated with the greatest severity. Despite recent advances on the molecular basis of elevated pathogenicity using recombinant proteins, the architecture of intact Delta virions remains veiled. Moreover, pieces of molecular evidence for the detailed mechanism of S-mediated membrane fusion are missing. Here, we showed the pleomorphic nature of Delta virions from electron beam inactivated samples and reported the in situ structure and distribution of S on the authentic Delta variant. We also captured the virus-virus fusion events, which provided pieces of structural evidence for Delta's attenuated dependency on cellular factors for fusion activation, and proposed a model of S-mediated membrane fusion. Besides, site-specific glycan analysis revealed increased oligomannose-type glycosylation of native Delta S than that of the WT S. Together, these results disclose distinctive factors of Delta being the most virulent SARS-CoV-2 variant.
External linksProc Natl Acad Sci U S A / PubMed:37094167 / PubMed Central
MethodsEM (single particle) / EM (subtomogram averaging)
Resolution4.39 - 13.0 Å
Structure data

33205

7y6d

EMDB-33205: Cryo-EM structure of SARS-CoV-2 Delta variant prefusion S in closed conformation
PDB-7y6d: Cryo-EM structure of SARS-CoV-2 Delta variant spike proteins on intact virions: 3 Closed RBD
Method: EM (single particle) / Resolution: 4.4 Å

EMDB-33206: Subtomogram average of SARS-CoV-2 Delta variant prefusion S in closed conformation.
Method: EM (subtomogram averaging) / Resolution: 9.8 Å

EMDB-33207: Subtomogram average of SARS-CoV-2 Delta variant prefusion S in one RBD up conformation.
Method: EM (subtomogram averaging) / Resolution: 13.0 Å

EMDB-33208: Subtomogram average of SARS-CoV-2 Delta variant postfusion S.
Method: EM (subtomogram averaging) / Resolution: 11.9 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / trimer

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