8IV4 | pdb_00008iv4

Cryo-EM structure of SARS-CoV-2 spike protein in complex with double nAbs 8H12 and 3E2 (local refinement)

• PDB DOI: https://doi.org/10.2210/pdb8IV4/pdb
• EM Map EMD-35740: EMDB EMDataResource

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


• Deposited: 2023-03-26 Released: 2023-08-16 
• Deposition Author(s): Sun, H., Jiang, Y., Zheng, Q., Li, S., Xia, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Two antibodies show broad, synergistic neutralization against SARS-CoV-2 variants by inducing conformational change within the RBD.

Sun, H., Deng, T., Zhang, Y., Lin, Y., Jiang, Y., Jiang, Y., Huang, Y., Song, S., Cui, L., Li, T., Xiong, H., Lan, M., Liu, L., Li, Y., Fang, Q., Yu, K., Jiang, W., Zhou, L., Que, Y., Zhang, T., Yuan, Q., Cheng, T., Zhang, Z., Yu, H., Zhang, J., Luo, W., Li, S., Zheng, Q., Gu, Y., Xia, N.

(2024) Protein Cell 15: 121-134

• PubMed: 37470320 
• DOI: https://doi.org/10.1093/procel/pwad040
• Primary Citation Related Structures: 
  8IV4, 8IV5, 8IV8, 8IVA


• PubMed Abstract: 
  

  Continual evolution of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) virus has allowed for its gradual evasion of neutralizing antibodies (nAbs) produced in response to natural infection or vaccination. The rapid nature of these changes has incited a need for the development of superior broad nAbs (bnAbs) and/or the rational design of an antibody cocktail that can protect against the mutated virus strain. Here, we report two angiotensin-converting enzyme 2 competing nAbs-8H12 and 3E2-with synergistic neutralization but evaded by some Omicron subvariants. Cryo-electron microscopy reveals the two nAbs synergistic neutralizing virus through a rigorous pairing permitted by rearrangement of the 472-489 loop in the receptor-binding domain to avoid steric clashing. Bispecific antibodies based on these two nAbs tremendously extend the neutralizing breadth and restore neutralization against recent variants including currently dominant XBB.1.5. Together, these findings expand our understanding of the potential strategies for the neutralization of SARS-CoV-2 variants toward the design of broad-acting antibody therapeutics and vaccines.

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Organizational Affiliation: 
• State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China.
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 Vaccines for Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China.
Xiang An Biomedicine Laboratory, Xiamen 361102, China.
Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, China.
The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, China.
Research Unit of Frontier Technology of Structural Vaccinology, Chinese Academy of Medical Sciences, Xiamen 361102, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 72.85 kDa 
• Atom Count: 5,027 
• Modeled Residue Count: 644 
• Deposited Residue Count: 655 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of 3E2	A [auth L]	104	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of 3E2	B [auth H]	121	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of 8H12	C [auth B]	107	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of 8H12	D [auth A]	119	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	E [auth G]	204	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Oligosaccharides

Help  

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-16 
Deposition Author(s): Sun, H., Jiang, Y., Zheng, Q., Li, S., Xia, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-08-16
  Type: Initial release
  
• Version 1.1: 2024-02-14
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Structure summary