9DKK | pdb_00009dkk

Designed miniproteins potently inhibit and protect against MERS-CoV. MERS-CoV S in complex with miniprotein cb3_GGGSGGGS_SB175, linker 7 (Local refinement of two RBDs and 2 miniproteins)

• PDB DOI: https://doi.org/10.2210/pdb9DKK/pdb
• EM Map EMD-46960: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Middle East respiratory syndrome-related coronavirus, synthetic construct
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-09 Released: 2025-10-15 
• Deposition Author(s): Tortorici, M.A., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
• 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: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Designed miniproteins potently inhibit and protect against MERS-CoV.

Ragotte, R.J., Tortorici, M.A., Catanzaro, N.J., Addetia, A., Coventry, B., Froggatt, H.M., Lee, J., Stewart, C., Brown, J.T., Goreshnik, I., Sims, J.N., Milles, L.F., Wicky, B.I.M., Glogl, M., Gerben, S., Kang, A., Bera, A.K., Sharkey, W., Schafer, A., Harkema, J.R., Baric, R.S., Baker, D., Veesler, D.

(2025) Cell Rep 44: 115760-115760

• PubMed: 40450691 
• DOI: https://doi.org/10.1016/j.celrep.2025.115760
• Primary Citation of Related Structures:  
  9C7Z, 9DGO, 9DKK


• PubMed Abstract: 
  

  Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic pathogen with a 36% case-fatality rate in humans. No vaccines or specific therapeutics are currently approved for use in humans or the camel host reservoir. Here, we computationally designed monomeric and homo-oligomeric miniproteins that bind with high affinity to the MERS-CoV spike (S) glycoprotein, the main target of neutralizing antibodies and vaccine development. We show that these miniproteins broadly neutralize a panel of MERS-CoV S variants, spanning the known antigenic diversity of this pathogen, by targeting a conserved site in the receptor-binding domain (RBD). The miniproteins directly compete with binding of the dipeptidylpeptidase 4 (DPP4) receptor to MERS-CoV S, thereby blocking viral attachment to the host entry receptor and subsequent membrane fusion. Intranasal administration of a lead miniprotein provides prophylactic protection against stringent MERS-CoV challenge in mice, motivating its future clinical development as a next-generation countermeasure against this virus with pandemic potential.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA.
Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI 48824, USA.
Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA. Electronic address: [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. Electronic address: [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 334.57 kDa 
• Atom Count: 3,782 
• Modeled Residue Count: 515 
• Deposited Residue Count: 3,020 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein	A [auth B], C [auth A]	1,366	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Miniprotein cb3_GGGSGGGS_SB175	B [auth D], D [auth C]	144	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	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 (Subject of Investigation/LOI)	G [auth B], H [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: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419:
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Tortorici, M.A., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.

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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: 2025-10-15
  Type: Initial release
  
• Version 1.1: 2026-02-25
  Changes: Data collection, Database references