7KL9 | pdb_00007kl9

Structure of the SARS-CoV-2 S 6P trimer in complex with the ACE2 protein decoy, CTC-445.2 (State 4)

• PDB DOI: https://doi.org/10.2210/pdb7KL9/pdb
• EM Map EMD-22916: EMDB EMDataResource

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens, Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2020-10-29 Released: 2020-11-11 
• Deposition Author(s): Barnes, C.O., Bjorkman, P.J.
• 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: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2.

Linsky, T.W., Vergara, R., Codina, N., Nelson, J.W., Walker, M.J., Su, W., Barnes, C.O., Hsiang, T.Y., Esser-Nobis, K., Yu, K., Reneer, Z.B., Hou, Y.J., Priya, T., Mitsumoto, M., Pong, A., Lau, U.Y., Mason, M.L., Chen, J., Chen, A., Berrocal, T., Peng, H., Clairmont, N.S., Castellanos, J., Lin, Y.R., Josephson-Day, A., Baric, R.S., Fuller, D.H., Walkey, C.D., Ross, T.M., Swanson, R., Bjorkman, P.J., Gale Jr., M., Blancas-Mejia, L.M., Yen, H.L., Silva, D.A.

(2020) Science 370: 1208-1214

• PubMed: 33154107 
• DOI: https://doi.org/10.1126/science.abe0075
• Primary Citation Related Structures: 
  7KL9


• PubMed Abstract: 
  

  We developed a de novo protein design strategy to swiftly engineer decoys for neutralizing pathogens that exploit extracellular host proteins to infect the cell. Our pipeline allowed the design, validation, and optimization of de novo human angiotensin-converting enzyme 2 (hACE2) decoys to neutralize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The best monovalent decoy, CTC-445.2, bound with low nanomolar affinity and high specificity to the receptor-binding domain (RBD) of the spike protein. Cryo-electron microscopy (cryo-EM) showed that the design is accurate and can simultaneously bind to all three RBDs of a single spike protein. Because the decoy replicates the spike protein target interface in hACE2, it is intrinsically resilient to viral mutational escape. A bivalent decoy, CTC-445.2d, showed ~10-fold improvement in binding. CTC-445.2d potently neutralized SARS-CoV-2 infection of cells in vitro, and a single intranasal prophylactic dose of decoy protected Syrian hamsters from a subsequent lethal SARS-CoV-2 challenge.

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Organizational Affiliation: 
• Neoleukin Therapeutics Inc., Seattle, WA, USA.
School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China.
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA, USA.
Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA.
Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Department of Microbiology, University of Washington, Seattle, WA, USA.
Department of Infectious Diseases, University of Georgia, Athens, GA, USA.
Neoleukin Therapeutics Inc., Seattle, WA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 476.49 kDa 
• Atom Count: 26,358 
• Modeled Residue Count: 3,468 
• Deposited Residue Count: 4,251 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,257	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2 Membrane Entity: Yes
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 10		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CTC-445.2 inhibitor	D [auth E], E [auth D], F	160	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H	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	AA [auth B], BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], I [auth A], IA [auth C], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	v2.14

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-11 
Deposition Author(s): Barnes, C.O., Bjorkman, P.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01-AI13893

Revision History  

• Version 1.0: 2020-11-11
  Type: Initial release
  
• Version 1.1: 2020-11-25
  Changes: Database references
• Version 1.2: 2020-12-16
  Changes: Database references
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2025-06-04
  Changes: Data collection