9Z3J | pdb_00009z3j

HCoV-NL63 S2' peptide bound to TMPRSS2 S441A (complexed with the H1H7 Fab and an anti-kappa-nanobody)

• PDB DOI: https://doi.org/10.2210/pdb9Z3J/pdb
• EM Map EMD-73786: EMDB EMDataResource

• Classification: VIRAL PROTEIN/Immune System
• Organism(s): Human coronavirus NL63, Homo sapiens, Lama glama
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-11-06 Released: 2026-05-13 
• Deposition Author(s): McCallum, M., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
• 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

TMPRSS2-mediated coronavirus spike activation and inhibition.

McCallum, M., Case, J.B., Brown, J.T., Park, Y.J., Lee, J., Sutherland, E., Aggarwal, A., Gibson, C., Lempp, F.A., Stewart, C., Tortorici, M.A., Sanapala, S., Low, J.S., Asarnow, D., Bohan, D., Dellota Jr., E., Merz, B., Chawla, B., Kar, S., Lanzavecchia, A., Sallusto, F., Riley, N.M., Turville, S., Purcell, L., Diamond, M.S., Veesler, D.

(2026) Nat Struct Mol Biol 

• PubMed: 42050172 
• DOI: https://doi.org/10.1038/s41594-026-01801-y
• Primary Citation Related Structures: 
  11HK, 11HL, 11HN, 11HW, 9OPQ, 9OPR, 9YYU, 9YYV, 9Z3J, 9Z3K


• PubMed Abstract: 
  

  The protease TMPRSS2 facilitates coronavirus infections, yet its mechanism of viral glycoprotein recognition remains unclear. Here we show that, following ACE2 engagement of the SARS-CoV-2 spike (S) inducing the early fusion intermediate conformation (E-FIC), TMPRSS2 cleaves the R815 S ₂ ' site and promotes fusogenic conformational changes leading to viral entry. We unveil TMPRSS2 recognition of S ₂ ', identify key residues modulating binding specificity and demonstrate that S ₂ ' site-directed broadly neutralizing antibodies target E-FIC and inhibit viral entry by blocking TMPRSS2 access. We computationally designed stabilized E-FIC as a vaccine candidate, overcoming the transient nature of this state. We describe a TMPRSS2-directed monoclonal antibody inhibiting several coronaviruses, including SARS-CoV-2 variants and protecting mice against SARS-CoV-2 challenge. These results outline the mechanistic role of TMPRSS2 and S ₂ ' site-directed antibodies in coronavirus entry.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA, USA.
Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada.
Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
Howard Hughes Medical Institute, Seattle, WA, USA.
Department of Chemistry, University of Washington, Seattle, WA, USA.
The Kirby Institute, The University of New South Wales, Sydney, New South Wales, Australia.
Vir Biotechnology, San Francisco, CA, USA.
Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.
Institute of Microbiology, ETH Zürich, Zurich, Switzerland.
A*STAR Infectious Diseases Labs (A*STAR IDL), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
Bioqual, Rockville, MD, USA.
Vir Biotechnology, Bellinzona, Switzerland.
National Institute of Molecular Genetics, Milano, Italy.
Third Rock Ventures, Boston, MA, USA.
Department of Medicine, 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, Seattle, WA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A3B1C1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 124.88 kDa 
• Atom Count: 6,773 
• Modeled Residue Count: 895 
• Deposited Residue Count: 1,130 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HCoV-NL63 S2' peptide	A	15	Human coronavirus NL63	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for Q6Q1S2 (Human coronavirus NL63) Explore Q6Q1S2  Go to UniProtKB:  Q6Q1S2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Inactive TMPRSS2 construct	B	519	Homo sapiens	Mutation(s): 1  Gene Names: AZU1, SMT3, YDR510W, D9719.15, TMPRSS2, PRSS10 EC: 3.4.21.122
UniProt & NIH Common Fund Data Resources
Find proteins for O15393 (Homo sapiens) Explore O15393  Go to UniProtKB:  O15393
PHAROS:  O15393 GTEx:  ENSG00000184012
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: O15393-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H1H7 heavy chain	C [auth H]	223	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
H1H7 light chain	D [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-kappa nanobody	E [auth N]	159	Lama glama	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth C]	3		N-Glycosylation

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: 2026-05-13 
Deposition Author(s): McCallum, M., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.

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

Revision History  

• Version 1.0: 2026-05-13
  Type: Initial release