9XZX | pdb_00009xzx

Staphylococcal Enterotoxin C in complex with NB C107 and NB C112

• PDB DOI: https://doi.org/10.2210/pdb9XZX/pdb
• EM Map EMD-72377: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Staphylococcus aureus, Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-08-27 Released: 2026-05-06 
• Deposition Author(s): Hang, W., Kim, J., Taylor, D.J., Shi, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Multivalent nanobodies for potent and broad neutralization of Staphylococcus aureus toxins.

Kim, Y.J.J., Walton, N.R., Huang, W., Lee, M., Xiang, Y., Sang, Z., Sussman, C., Moore, S.K.L., Taylor, D.J., Chen, K., Hook, J.L., McCormick, J.K., Shi, Y.

(2026) Nat Commun 17

• PubMed: 42161902 
• DOI: https://doi.org/10.1038/s41467-026-73120-1
• Primary Citation Related Structures: 
  9XZX


• PubMed Abstract: 
  

  Staphylococcus aureus is a leading cause of lethal bacteremia and pneumonia, which are driven by potent virulence factors such as T-cell superantigens and alpha hemolysin. S. aureus has among the highest rates of antibiotic resistance, yet no vaccines or alternative therapies are available. Here, we developed a repertoire of potent, high-affinity nanobodies (Nbs) targeting key toxins in S. aureus infection, including Hla and superantigens SEB, SEC, and TSST-1. Comprehensive cryo-EM and AlphaFold3 analyses of these Nbs, which were elicited with clinical cocktail vaccines, revealed diverse neutralizing epitopes and mechanisms that provide insights for immunotherapy and vaccine strategies. Guided by these findings, we engineered stable, multivalent, and multifunctional Nb constructs. These constructs included an aerosolizable trimeric Nb with enhanced neutralization activity against Hla and SEC, and a decameric Nb-IgG-Fc fusion construct with pM or better potencies against a wide range of major toxins in S. aureus sepsis (SEB, SEC, TSST-1, and Hla). These multifunctional Nbs demonstrated protective activity in murine models of pneumonia and sepsis, underscoring their potential as versatile immunotherapies that address the complex virulence of S. aureus. Our work lays a foundation for precision immunotherapies beyond current treatment options to combat complex bacterial infections with multiple virulence mechanisms.

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Organizational Affiliation: 
• Center for Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada.
Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA.
Stony Brook University, New York, NY, USA.
Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Center for Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 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 and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 53.48 kDa 
• Atom Count: 3,734 
• Modeled Residue Count: 474 
• Deposited Residue Count: 476 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enterotoxin type C-2	A	236	Staphylococcus aureus	Mutation(s): 0  Gene Names: entC2
UniProt
Find proteins for P34071 (Staphylococcus aureus) Explore P34071  Go to UniProtKB:  P34071

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NB C107	B [auth C]	116	Lama glama	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NB C112	C [auth D]	124	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC	4.7.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-06 
Deposition Author(s): Hang, W., Kim, J., Taylor, D.J., Shi, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM154832

Revision History  

• Version 1.0: 2026-05-06
  Type: Initial release
  
• Version 1.1: 2026-06-03
  Changes: Data collection, Database references