Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A3B3C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A5B3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 502.64 kDa 
• Atom Count: 29150 
• Modelled Residue Count: 3697 
• Deposited Residue Count: 4509 
• Unique protein chains: 3

7WHK

The state 3 complex structure of Omicron spike with Bn03 (2-up RBD, 5 nanobodies)

• PDB DOI: 10.2210/pdb7WHK/pdb
• EM Map EMD-32503:EMDBEMDataResource

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


• Deposited: 2021-12-30 Released: 2022-05-11 
• Deposition Author(s): Zhan, W.Q., Zhang, X., Chen, Z.G., Sun, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.01 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Broad neutralization of SARS-CoV-2 variants by an inhalable bispecific single-domain antibody.

Li, C., Zhan, W., Yang, Z., Tu, C., Hu, G., Zhang, X., Song, W., Du, S., Zhu, Y., Huang, K., Kong, Y., Zhang, M., Mao, Q., Gu, X., Zhang, Y., Xie, Y., Deng, Q., Song, Y., Chen, Z., Lu, L., Jiang, S., Wu, Y., Sun, L., Ying, T.

(2022) Cell 185: 1389-1401.e18

• PubMed: 35344711 
• DOI: 10.1016/j.cell.2022.03.009
• Primary Citation of Related Structures:  
  7WHI, 7WHJ, 7WHK


• PubMed Abstract: 
  

The effectiveness of SARS-CoV-2 vaccines and therapeutic antibodies have been limited by the continuous emergence of viral variants and by the restricted diffusion of antibodies from circulation into the sites of respiratory virus infection. Here, we report the identification of two highly conserved regions on the Omicron variant receptor-binding domain recognized by broadly neutralizing antibodies. Furthermore, we generated a bispecific single-domain antibody that was able to simultaneously and synergistically bind these two regions on a single Omicron variant receptor-binding domain as revealed by cryo-EM structures. We demonstrated that this bispecific antibody can be effectively delivered to lung via inhalation administration and exhibits exquisite neutralization breadth and therapeutic efficacy in mouse models of SARS-CoV-2 infections. Importantly, this study also deciphered an uncommon and highly conserved cryptic epitope within the spike trimeric interface that may have implications for the design of broadly protective SARS-CoV-2 vaccines and therapeutics.

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Organizational Affiliation: 

MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, The Fifth People's Hospital of Shanghai, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai 200032, China. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1285	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 39  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bn03_nano2	D, H	120	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Bn03_nano1	E, F, G	138	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.01 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2021-12-30 
• Released Date: 2022-05-11 
Deposition Author(s): Zhan, W.Q., Zhang, X., Chen, Z.G., Sun, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81900729

Revision History  

• Version 1.0: 2022-05-11
  Type: Initial release