9C7S | pdb_00009c7s

Cryo EM structure of SARS-COV-2 (BQ 1.1) RBD in complex with Fab COV2-3891 (local refine)

• PDB DOI: https://doi.org/10.2210/pdb9C7S/pdb
• EM Map EMD-45287: EMDB EMDataResource

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


• Deposited: 2024-06-11 Released: 2025-10-08 
• Deposition Author(s): Binshtein, E., Crowe, J.E.
• Funding Organization(s): Defense Advanced Research Projects Agency (DARPA)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Epitope-focused discovery of SARS-CoV-2 antibodies that potently neutralize Omicron variants.

Zost, S.J., Suryadevara, N., Williamson, L.E., Scheaffer, S.M., Binshtein, E., Buchman, C.D., Johnson, N.V., Catanzaro, N.J., Ravera, S., Chapman, N.S., Myers, L., Ramamohan, A.R., Handal, L.S., Nguyen, D.C., Trivette, A., Martinez, J.R., Villalobos, E., Rutherford, S.A., Eun-Hyung Lee, F., Schafer, A., Baric, R.S., McLellan, J.S., Diamond, M.S., Carnahan, R.H., Crowe Jr., J.E.

(2026) Nat Microbiol 11: 1113-1132

• PubMed: 41820555 
• DOI: https://doi.org/10.1038/s41564-026-02282-x
• Primary Citation Related Structures: 
  9C6Y, 9C7S, 9NVG


• PubMed Abstract: 
  

  The emergence of SARS-CoV-2 Omicron variants has led to viral escape from many clinically approved monoclonal antibodies (mAbs) due to rapid evolution of the receptor-binding domain (RBD). Co-circulation of SARS-CoV-2 variants with unique sets of antigenic substitutions has further complicated therapeutic mAb discovery. New approaches are needed to rapidly discover and characterize mAbs with preferred specificity and functional characteristics. Here we describe and perform epitope-focused mAb discovery using glycan-masked antigens. We isolated and expressed a panel of 303 mAbs, some of which potently neutralize divergent Omicron subvariants by targeting the class 3 antigenic site on SARS-CoV-2 RBD. Epitope mapping of these antibodies revealed a spectrum of cross-reactivity and differential recognition of the class 3 site, validating the utility of this enrichment approach for targeted mAb discovery. Together, this work rationally designs glycan-masked engineered RBDs and uses them to isolate mAbs that potently neutralize antigenically divergent SARS-CoV-2 variants.

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Organizational Affiliation: 
• The Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN, USA.
Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
Department of Medicine, Washington University School of Medicine, StLouis, MO, USA.
Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
Department of Medicine, Emory University, Atlanta, GA, USA.
Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
The Andrew M. Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA.
The Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN, USA. [e-mail].
Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA. [e-mail].
Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA. [e-mail].

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 and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 54.53 kDa 
• Atom Count: 3,837 
• Modeled Residue Count: 491 
• Deposited Residue Count: 491 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2'	A [auth C]	268	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab COV-3891 heavy chain	B [auth H]	116	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab COV-3891 light chain	C [auth L]	107	Homo sapiens	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Binshtein, E., Crowe, J.E.

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Funding Organization	Location	Grant Number
Defense Advanced Research Projects Agency (DARPA)	United States	HR0011-18-2-0001

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release
  
• Version 1.1: 2026-04-22
  Changes: Data collection, Database references