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 9KVE | pdb_00009kve

Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 4H1, 4A5 and 4C1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history. 

Literature

Broad neutralizing antibody response of a monomeric spike-based SARS-CoV-2 bivalent vaccine against diverse variants.

Wang, S., Sun, H., Wang, Y., Wang, Z., Yuan, L., Guo, H., Gao, J., Lan, M., Wu, Y., Shang, H., Chen, X., Chen, Z., Hu, J., Tang, Z., Wen, G., Ying, D., Liu, C., Jiang, Y., Su, J., Lin, M., Wu, T., Li, S., Zhang, T., Zhang, J., Guan, Y., Xia, N., Yuan, Q., Zheng, Q., Zhang, Y., Zheng, Z.

(2025) Proc Natl Acad Sci U S A 122: e2503254122-e2503254122

  • DOI: https://doi.org/10.1073/pnas.2503254122
  • Primary Citation Related Structures: 
    9KVD, 9KVE, 9KVF

  • PubMed Abstract: 

    severeacute respiratory syndrome coronavirus 2 (SARS-CoV-2) bivalent vaccines show potential against variants but lack a full understanding of the immunological mechanisms that drive broadly neutralizing antibodies (bnAbs). This study explored the immunogenicity of a bivalent vaccine in rhesus macaques, containing spike (S) proteins from the prototype (S prototype ) and chimeric S protein (S 1628x ). The vaccine induced bnAbs against multiple variants, including challenging subvariants like EG.1, BA.2.86, and JN.1. The monomeric S protein exposed less accessible regions within the receptor-binding domain (RBD) "inner face" and "NTD face" and subdomains 1, eliciting a diverse array of bnAbs against various Omicron subvariants. Notably, antibodies targeting the conserved RBD inner face, such as 4A5, showed potent neutralization across all tested variants. Structural analyses provide insights into the broad protectiveness of these vaccine-elicited nAbs. This study underscores the potential of bivalent vaccines with monomeric spike proteins to confer broad-spectrum immunity, offering a promising direction for future SARS-CoV-2 universal vaccine design.


  • Organizational Affiliation: 
    • State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361102, China.

Macromolecule Content 

  • Total Structure Weight: 97.9 kDa 
  • Atom Count: 6,728 
  • Modeled Residue Count: 894 
  • Deposited Residue Count: 895 
  • Unique protein chains: 7

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
The heavy chain of 4C1128Macaca mulattaMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
The light chain of 4C1110Macaca mulattaMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
The heavy chain of 4A5C [auth E]123Macaca mulattaMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
The light chain of 4A5D [auth G]107Macaca mulattaMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike protein S1E [auth C]194Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
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UniProt GroupP0DTC2
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
The heavy chain of 4H1F [auth D]120Macaca mulattaMutation(s): 0 
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
The light chain of 4H1G [auth F]113Macaca mulattaMutation(s): 0 
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release
  • Version 1.1: 2026-09-02
    Changes: Data collection, Database references