11HK | pdb_000011hk

SARS-CoV-2 spike S2 trimer stabilized in the early fusion intermediate conformation (E-FICs-v3) bound to the VN01H1 Fab (Fab local refinement)

• PDB DOI: https://doi.org/10.2210/pdb11HK/pdb
• EM Map EMD-75694: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C, Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2026-02-24 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: 2.70 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: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 9-mer - A6B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 347.32 kDa 
• Atom Count: 9,288 
• Modeled Residue Count: 1,254 
• Deposited Residue Count: 3,138 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E-FICS-v3	A, D, G	605	Saccharomyces cerevisiae S288C, Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: SMT3, YDR510W, D9719.15, S, 2
UniProt
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306  Go to UniProtKB:  Q12306
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
UniProt Groups	P0DTC2Q12306
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q12306-1P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of VN01H1 Fab	B, E, H	226	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of VN01H1 Fab	C, F, I	215	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], K [auth A], L [auth D], M [auth D], N [auth G], O [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 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