8JVA | pdb_00008jva

Cryo-EM structure of the N-terminal domain of Omicron BA.1 in complex with nanobody N235 and S2L20 Fab

• PDB DOI: https://doi.org/10.2210/pdb8JVA/pdb
• EM Map EMD-36672: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Vicugna pacos, Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2023-06-28 Released: 2024-05-22 
• Deposition Author(s): Liu, B., Liu, H.H., Han, P., Qi, J.X.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.81 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Enhanced potency of an IgM-like nanobody targeting conserved epitope in SARS-CoV-2 spike N-terminal domain.

Liu, B., Liu, H., Han, P., Wang, X., Wang, C., Yan, X., Lei, W., Xu, K., Zhou, J., Qi, J., Fan, R., Wu, G., Tian, W.X., Gao, G.F., Wang, Q.

(2024) Signal Transduct Target Ther 9: 131-131

• PubMed: 38740785 
• DOI: https://doi.org/10.1038/s41392-024-01847-8
• Primary Citation Related Structures: 
  8JVA


• PubMed Abstract: 
  

  Almost all the neutralizing antibodies targeting the receptor-binding domain (RBD) of spike (S) protein show weakened or lost efficacy against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged or emerging variants, such as Omicron and its sub-variants. This suggests that highly conserved epitopes are crucial for the development of neutralizing antibodies. Here, we present one nanobody, N235, displaying broad neutralization against the SARS-CoV-2 prototype and multiple variants, including the newly emerged Omicron and its sub-variants. Cryo-electron microscopy demonstrates N235 binds a novel, conserved, cryptic epitope in the N-terminal domain (NTD) of the S protein, which interferes with the RBD in the neighboring S protein. The neutralization mechanism interpreted via flow cytometry and Western blot shows that N235 appears to induce the S1 subunit shedding from the trimeric S complex. Furthermore, a nano-IgM construct (MN235), engineered by fusing N235 with the human IgM Fc region, displays prevention via inducing S1 shedding and cross-linking virus particles. Compared to N235, MN235 exhibits varied enhancement in neutralization against pseudotyped and authentic viruses in vitro. The intranasal administration of MN235 in low doses can effectively prevent the infection of Omicron sub-variant BA.1 and XBB in vivo, suggesting that it can be developed as a promising prophylactic antibody to cope with the ongoing and future infection.

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Organizational Affiliation: 
• College of Veterinary Medicine, Shanxi Agricultural University, 030801, Jinzhong, China.
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), 100101, Beijing, China.
School of Life Sciences, Yunnan University, 650504, Kunming, Yunnan Province, China.
NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), 102206, Beijing, China.
Savaid Medical School, University of Chinese Academy of Sciences, 101408, Beijing, China.
NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), 102206, Beijing, China. [e-mail].
College of Veterinary Medicine, Shanxi Agricultural University, 030801, Jinzhong, China. [e-mail].
College of Veterinary Medicine, Shanxi Agricultural University, 030801, Jinzhong, China. [e-mail].
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), 100101, Beijing, China. [e-mail].
College of Veterinary Medicine, Shanxi Agricultural University, 030801, Jinzhong, China. [e-mail].
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), 100101, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 127.21 kDa 
• Atom Count: 6,071 
• Modeled Residue Count: 769 
• Deposited Residue Count: 1,135 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody N235	A [auth D]	126	Vicugna pacos	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S2L20 light chain	B [auth A]	236	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
S2L20 heavy chain	C [auth B]	473	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2'	D [auth F]	300	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 4  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 5		Go to GlyGen: P0DTC2-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	E [auth F], F, G [auth F], H [auth F], I [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.81 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Liu, B., Liu, H.H., Han, P., Qi, J.X.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	82225021

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Structure summary
• Version 1.2: 2025-07-16
  Changes: Data collection