6ZXN | pdb_00006zxn

Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1)

• PDB DOI: https://doi.org/10.2210/pdb6ZXN/pdb
• EM Map EMD-11526: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Vicugna pacos
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-30 Released: 2020-09-23 
• Deposition Author(s): Hallberg, B.M., Das, H.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.93 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction.

Hanke, L., Vidakovics Perez, L., Sheward, D.J., Das, H., Schulte, T., Moliner-Morro, A., Corcoran, M., Achour, A., Karlsson Hedestam, G.B., Hallberg, B.M., Murrell, B., McInerney, G.M.

(2020) Nat Commun 11: 4420-4420

• PubMed: 32887876 
• DOI: https://doi.org/10.1038/s41467-020-18174-5
• Primary Citation Related Structures: 
  6ZXN


• PubMed Abstract: 
  

  SARS-CoV-2 enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. Ty1 binds the RBD with high affinity, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 Å resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the 'up' and 'down' conformations, sterically hindering RBD-ACE2 binding. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19.

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Organizational Affiliation: 
• Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
Division of Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden.
Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden. [e-mail].
Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany. [e-mail].
Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden. [e-mail].
Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 483.84 kDa 
• Atom Count: 28,335 
• Modeled Residue Count: 3,522 
• Deposited Residue Count: 4,266 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 17		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody Ty1	D, E, F	134	Vicugna pacos	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, I, J, K, L, M, N, O, P, Q, R	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 A], AB [auth C], BA [auth A], BB [auth C], CA [auth A], CB [auth C], DA [auth A], DB [auth C], EA [auth A], EB [auth C], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth B], RA [auth B], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth A], YA [auth C], Z [auth A], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.93 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.15
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-23 
Deposition Author(s): Hallberg, B.M., Das, H.

Revision History  

• Version 1.0: 2020-09-23
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Refinement description, Structure summary