9NVG | pdb_00009nvg

Structure of SARS-CoV-2 BA.1 spike RBD bound to COV2-3835 Fab

• PDB DOI: https://doi.org/10.2210/pdb9NVG/pdb
• EM Map EMD-49835: 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: 2025-03-20 Released: 2026-02-25 
• Deposition Author(s): Ramamohan, A.R., Johnson, N.V., McLellan, J.S.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 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.

---

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.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 191 kDa 
• Atom Count: 3,271 
• Modeled Residue Count: 413 
• Deposited Residue Count: 1,728 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	1,285	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 10  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COV2-3835 Fab Heavy Chain	B [auth H]	229	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
COV2-3835 Fab Light Chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21rc1_5127

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-25 
Deposition Author(s): Ramamohan, A.R., Johnson, N.V., McLellan, J.S.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-02-25
  Type: Initial release
  
• Version 1.1: 2026-04-29
  Changes: Data collection, Database references