9BJ2 | pdb_00009bj2

Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1533 (local refinement of NTD and C1533)

• PDB DOI: https://doi.org/10.2210/pdb9BJ2/pdb
• EM Map EMD-44627: EMDB EMDataResource

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


• Deposited: 2024-04-24 Released: 2025-03-05 
• Deposition Author(s): Rubio, A.A., Abernathy, M.E., Barnes, C.O.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.

Rubio, A.A., Baharani, V.A., Dadonaite, B., Parada, M., Abernathy, M.E., Wang, Z., Lee, Y.E., Eso, M.R., Phung, J., Ramos, I., Chen, T., El Nesr, G., Bloom, J.D., Bieniasz, P.D., Nussenzweig, M.C., Barnes, C.O.

(2025) Sci Transl Med 17: eadq5720-eadq5720

• PubMed: 40043139 
• DOI: https://doi.org/10.1126/scitranslmed.adq5720
• Primary Citation of Related Structures:  
  9BJ2, 9BJ3, 9BJ4


• PubMed Abstract: 
  

  The ongoing emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) that reduce the effectiveness of antibody therapeutics necessitates development of next-generation antibody modalities that are resilient to viral evolution. Here, we characterized amino-terminal domain (NTD)- and receptor binding domain (RBD)-specific monoclonal antibodies previously isolated from coronavirus disease 2019 (COVID-19) convalescent donors for their activity against emergent SARS-CoV-2 VOCs. Among these, the NTD-specific antibody C1596 displayed the greatest breadth of binding to VOCs, with cryo-electron microscopy structural analysis revealing recognition of a distinct NTD epitope outside of the site i antigenic supersite. Given C1596's favorable binding profile, we designed a series of bispecific antibodies (bsAbs), termed CoV2-biRNs, that featured both NTD and RBD specificities. Two of the C1596-inclusive bsAbs, CoV2-biRN5 and CoV2-biRN7, retained potent in vitro neutralization activity against all Omicron variants tested, including XBB.1.5, BA.2.86, and JN.1, contrasting the diminished potency of parental antibodies delivered as monotherapies or as a cocktail. Furthermore, prophylactic delivery of CoV2-biRN5 reduced the viral load within the lungs of K18-hACE2 mice after challenge with SARS-CoV-2 XBB.1.5. In conclusion, NTD-RBD bsAbs offer promising potential for the design of resilient, next-generation antibody therapeutics against SARS-CoV-2 VOCs.

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Organizational Affiliation: 
• Stanford Biosciences, Stanford School of Medicine, Stanford, CA 94305, USA.
Department of Biology, Stanford University, Stanford, CA 94305, USA.
Laboratory of Retrovirology, Rockefeller University, New York, NY 10065, USA.
Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA.
Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
Sarafan ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 195.77 kDa 
• Atom Count: 3,920 
• Modeled Residue Count: 501 
• Deposited Residue Count: 1,784 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 9  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C1533 Heavy Chain	B [auth H]	261	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
C1533 Light Chain	C [auth L]	235	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-05 
Deposition Author(s): Rubio, A.A., Abernathy, M.E., Barnes, C.O.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	GT15335

Revision History  

• Version 1.0: 2025-03-05
  Type: Initial release
  
• Version 1.1: 2025-03-19
  Changes: Data collection, Database references