7WP6 | pdb_00007wp6

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

PDB DOI: https://doi.org/10.2210/pdb7WP6/pdb
EM Map EMD-32676: EMDB EMDataResource

Classification: IMMUNE SYSTEM/VIRAL PROTEIN
Organism(s): Mus musculus, Severe acute respiratory syndrome coronavirus 2
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2022-01-23 Released: 2023-03-01
Deposition Author(s): Zheng, Q., Sun, H., Yuan, Q., Li, S., Xia, N.
Funding Organization(s): Not funded

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 1.3 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

PubMed: 36323313 Search on PubMedSearch on PubMed Central
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.

State Key Laboratory of Emerging Infectious Diseases, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong 515063, China; EKIH Pathogen Research Institute, Futian District, Shenzhen, Guangdong 518045, China.

Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, National Health Commission, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350013, China.

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. Electronic address: zhangtianying@xmu.edu.cn.

Macromolecule Content

Total Structure Weight: 96.46 kDa
Atom Count: 6,748
Modeled Residue Count: 861
Deposited Residue Count: 867
Unique protein chains: 7

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
36H6 heavy chain	A [auth B]	119	Mus musculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
83H7 light chain	B [auth C]	104	Mus musculus	Mutation(s): 0
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
83H7 heavy chain	C [auth D]	118	Mus musculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	D [auth F]	189	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D [auth F]	Go to GlyGen: P0DTC2-1
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
85F7 heavy chain	E [auth H]	118	Mus musculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
36H6 light chain	F [auth I]	113	Mus musculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
85F7 light chain	G [auth L]	106	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain G [auth L]
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Reference Sequence

Oligosaccharides

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Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth A]	2		N-Glycosylation	Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth L] MOL2 format, chain I [auth L] mmCIF format, chain I [auth L]	I [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth L] Interactions & Density Focus chain I [auth L]