9MR2 | pdb_00009mr2

SARS-CoV-2 S2 monomer in complex with NICA01A-1401 Fab

• PDB DOI: https://doi.org/10.2210/pdb9MR2/pdb
• EM Map EMD-48550: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2025-01-06 Released: 2025-11-26 
• Deposition Author(s): Park, S., Bangaru, B., Ward, A.B.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.79 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Common cold embecovirus imprinting primes broadly neutralizing antibody responses to SARS-CoV-2 S2.

Changrob, S., Yasuhara, A., Park, S., Bangaru, S., Li, L., Troxell, C.A., Halfmann, P.J., Erickson, S.A., Catanzaro, N.J., Yuan, M., Zhou, P., Huang, M., Wilbanks, G.D., McGrath, J.J.C., Singh, G., Nelson, S.A., Fu, Y., Zheng, N.Y., Carayannopoulos, S.M., Dugan, H.L., Shaw, D.G., Stamper, C.T., Madariaga, M.L.L., Krammer, F., Andrabi, R., Burton, D.R., Ward, A.B., Wilson, I.A., Kawaoka, Y., Wilson, P.C.

(2025) J Exp Medicine 222

• PubMed: 41066082 
• DOI: https://doi.org/10.1084/jem.20251146
• Primary Citation Related Structures: 
  9MR1, 9MR2


• PubMed Abstract: 
  

  The S2 subunit of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is highly conserved across coronavirus strains and therefore is a potential pan-coronavirus vaccine target. However, antibodies targeting this region are typically non-neutralizing. We report herein that S2-targeting antibodies from patients who recovered from SARS-CoV-2 infection bound only closely related sarbecovirus subgenus strains and, like most known S2 antibodies, none of these were neutralizing. In contrast, first-exposure, severe acutely infected COVID-19 patients predominantly induced back-boosted antibody-secreting cells imprinted against past common cold coronavirus strain OC43 that were cross-reactive to as many as five subgenera of betacoronavirus strains and gave rise to antibodies that were neutralizing and protective. The antibodies targeted two different sites: one defined by competition with stem helix antibodies, and the second to an underdescribed epitope at the apex of S2. These findings suggest that S2-targeted vaccines could strategically exploit controlled OC43 priming followed by SARS-CoV-2 boosting to enhance the breadth and quality of protective antibody responses.

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Organizational Affiliation: 
• Drukier Institute for Children's Health, Weill Cornell Medicine , New York, NY, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison , Madison, WI, USA.
University of Chicago Department of Medicine, Section of Rheumatology , Chicago, IL, USA.
Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Department of Immunology and Microbiology, IAVI Neutralizing Antibody Center and Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.
Center for Vaccine Research and Pandemic Preparedness, Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, NY, USA.
Department of Surgery, University of Chicago, Chicago, IL, USA.
Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna , Vienna, Austria.
Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University , Cambridge, MA, USA.
The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, CA, USA.
Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, Japan.

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: 77.14 kDa 
• Atom Count: 3,103 
• Modeled Residue Count: 407 
• Deposited Residue Count: 706 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NICA01A-1401 Fab Heavy chain	A	122	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NICA01A-1401 Fab Light chain	B	110	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2	C	474	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 11  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.79 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Rosetta
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Park, S., Bangaru, B., Ward, A.B.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	INV-004923

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release