9CWQ | pdb_00009cwq

Local refinement of the SARS-CoV-2 BA.2.86 NTD

• PDB DOI: https://doi.org/10.2210/pdb9CWQ/pdb
• EM Map EMD-45971: EMDB EMDataResource

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


• Deposited: 2024-07-30 Released: 2026-01-21 
• Deposition Author(s): Lee, J., Veesler, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

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

Literature

The computationally designed TRI2-2 miniprotein inhibitor protects against multiple SARS-CoV-2 Omicron variants.

Lee, J., Case, J.B., Park, Y.J., Ravichandran, R., Asarnow, D., Tortorici, M.A., Brown, J.T., Sanapala, S., Carter, L., Baker, D., Diamond, M.S., Veesler, D.

(2026) Commun Biol 9: 224-224

• PubMed: 41519898 
• DOI: https://doi.org/10.1038/s42003-025-09499-2
• Primary Citation Related Structures: 
  9CWP, 9CWQ, 9CWR


• PubMed Abstract: 
  

  The continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has compromised neutralizing antibody responses elicited by prior infection or vaccination and abolished the utility of most monoclonal antibody therapeutics. We previously described a computationally-designed, homotrimeric miniprotein inhibitor, designated TRI2-2, that protects mice against pre-Omicron SARS-CoV-2 variants. Here, we show that TRI2-2 exhibits broadly neutralizing activity of SARS-CoV-2 variants and protects mice against BQ.1.1, XBB.1.5 and BA.2.86 challenge when administered intranasally post-exposure. The resistance of TRI2-2 to viral escape by most variants and the ability to deliver it directly to the upper airways highlight the potential of the multivalent miniprotein inhibitor as an alternative therapeutic modality.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA, USA.
Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA. [e-mail].
Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA. [e-mail].
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA. [e-mail].
Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA. [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 36.42 kDa 
• Atom Count: 2,014 
• Modeled Residue Count: 248 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BA.2.86 Spike protein NTD	A	304	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0

Oligosaccharides

Help  

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-01-21 
Deposition Author(s): Lee, J., Veesler, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI158186

Revision History  

• Version 1.0: 2026-01-21
  Type: Initial release
  
• Version 1.1: 2026-02-25
  Changes: Data collection, Database references