8ZYM | pdb_00008zym

Complex structure of 60 Fab bound to DS2 prefusion F trimer

• PDB DOI: https://doi.org/10.2210/pdb8ZYM/pdb
• EM Map EMD-60572: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Respiratory syncytial virus A2, synthetic construct, Mus musculus
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-06-18 Released: 2025-04-30 
• Deposition Author(s): Wang, X., Ge, J., Guo, F.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.23 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

DS2 designer pre-fusion F vaccine induces strong and protective antibody response against RSV infection.

Yang, Y., Wang, R., Guo, F., Zhao, T., Lei, Y., Yang, Q., Zeng, Y., Yang, Z., Ajavavarakula, T., Tan, R., Li, M., Dong, H., Niu, M., Bao, K., Geng, H., Lv, Q., Zhang, Q., Shi, X., Liu, P., Ge, J., Wang, X., Zhang, L.

(2024) NPJ Vaccines 9: 258-258

• PubMed: 39741146 
• DOI: https://doi.org/10.1038/s41541-024-01059-9
• Primary Citation of Related Structures:  
  8ZYM


• PubMed Abstract: 
  

  DS-Cav1, SC-TM, and DS2 are distinct designer pre-fusion F proteins (pre-F) of respiratory syncytial virus (RSV) developed for vaccines. However, their immunogenicity has not been directly compared. In this study, we generated three recombinant vaccines using the chimpanzee adenovirus vector AdC68 to express DS-Cav1, SC-TM, and DS2. All three vaccines elicited robust serum binding and neutralizing antibodies following intramuscular priming and boosting. DS2 induced the strongest antibody responses, followed by SC-TM and DS-Cav1. DS2 also provided strong protection against live RSV challenge. Monoclonal antibodies (mAbs) isolated from long-lived antibody-secreting cells (ASCs) in the bone marrow six months post-immunization with AdC68-DS2 predominantly targeted site Ø as well as site II. One neutralizing antibody against site II, mAb60, conferred strong protection against live RSV infection in mice. These findings highlight the strong ability of the DS2 design in eliciting long-lived antibody responses and guide the development of next-generation RSV vaccines.

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Organizational Affiliation: 
• Comprehensive AIDS Research Center, Pandemic Research Alliance Unit, Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, 100084, Beijing, China.
The Ministry of Education Key Laboratory of Protein Science, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, 100084, Beijing, China.
School of Biomedical Engineering, Tsinghua University, 100084, Beijing, China.
School of Biomedical Engineering, Tsinghua University, 100084, Beijing, China. [e-mail].
Changping Laboratory, 102206, Beijing, China. [e-mail].
State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, 102629, Beijing, China. [e-mail].
Key Laboratory of Pathogen Infection Prevention and Control (MOE), Ministry of Education, Chinese Academy of Medical Sciences & Peking Union Medical College, 102629, Beijing, China. [e-mail].
The Ministry of Education Key Laboratory of Protein Science, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, 100084, Beijing, China. [e-mail].
Comprehensive AIDS Research Center, Pandemic Research Alliance Unit, Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, 100084, Beijing, China. [e-mail].
Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, 518055, Shenzhen, China. [e-mail].
Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, 518132, Shenzhen, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 9-mer - A6B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 260.15 kDa 
• Atom Count: 15,829 
• Modeled Residue Count: 2,055 
• Deposited Residue Count: 2,373 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0,Expression tag	A, B, C	558	Respiratory syncytial virus A2, synthetic construct	Mutation(s): 12
UniProt
Find proteins for C3UPB8 (Respiratory syncytial virus) Explore C3UPB8  Go to UniProtKB:  C3UPB8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody light chain	D, E, F	112	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
antidody heavy chain	G, H, I	121	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.23 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-30 
Deposition Author(s): Wang, X., Ge, J., Guo, F.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release