7WP6

Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK in complex with three neutralizing antibodies


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Lineage-mosaic and mutation-patched spike proteins for broad-spectrum COVID-19 vaccine.

Wu, Y.Wang, S.Zhang, Y.Yuan, L.Zheng, Q.Wei, M.Shi, Y.Wang, Z.Ma, J.Wang, K.Nie, M.Xiao, J.Huang, Z.Chen, P.Guo, H.Lan, M.Xu, J.Hou, W.Hong, Y.Chen, D.Sun, H.Xiong, H.Zhou, M.Liu, C.Guo, W.Guo, H.Gao, J.Gan, C.Li, Z.Zhang, H.Wang, X.Li, S.Cheng, T.Zhao, Q.Chen, Y.Wu, T.Zhang, T.Zhang, J.Cao, H.Zhu, H.Yuan, Q.Guan, Y.Xia, N.

(2022) Cell Host Microbe 30: 1732-1744.e7

  • DOI: https://doi.org/10.1016/j.chom.2022.10.011
  • Primary Citation of Related Structures:  
    7WP6, 7WP8

  • PubMed Abstract: 

    SARS-CoV-2 spread in humans results in continuous emergence of new variants, highlighting the need for vaccines with broad-spectrum antigenic coverage. Using inter-lineage chimera and mutation-patch strategies, we engineered a recombinant monomeric spike variant (STFK1628x) that contains key regions and residues across multiple SAR-CoV-2 variants. STFK1628x demonstrated high immunogenicity and mutually complementary antigenicity to its prototypic form (STFK). In hamsters, a bivalent vaccine composed of STFK and STFK1628x elicited high titers of broad-spectrum neutralizing antibodies to 19 circulating SARS-CoV-2 variants, including Omicron sublineages BA.1, BA.1.1, BA.2, BA.2.12.1, BA.2.75, and BA.4/5. Furthermore, this vaccine conferred robust protection against intranasal challenges by either SARS-CoV-2 ancestral strain or immune-evasive Beta and Omicron BA.1. Strikingly, vaccination with the bivalent vaccine in hamsters effectively blocked within-cage virus transmission of ancestral SARS-CoV-2, Beta variant, and Omicron BA.1 to unvaccinated sentinels. Thus, our study provided insight and antigen candidates for the development of next-generation COVID-19 vaccines.


  • Organizational Affiliation

    State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
36H6 heavy chainA [auth B]119Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
83H7 light chainB [auth C]104Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
83H7 heavy chainC [auth D]118Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1D [auth F]189Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
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Go to UniProtKB:  P0DTC2
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UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
85F7 heavy chainE [auth H]118Mus musculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
36H6 light chainF [auth I]113Mus musculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
85F7 light chainG [auth L]106Mus musculusMutation(s): 0 
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Glycosylation
Glycosylation Sites: 1
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Oligosaccharides

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Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth A]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
I [auth L]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Structure summary