8G74 | pdb_00008g74

SARS-CoV-2 spike/Nb3 complex with 1 RBD up and 2 Nb3

• PDB DOI: https://doi.org/10.2210/pdb8G74/pdb
• EM Map EMD-29796: EMDB EMDataResource

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


• Deposited: 2023-02-16 Released: 2024-01-24 
• Deposition Author(s): Ye, G., Bu, F., Liu, B., Li, F.
• 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: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Discovery of Nanosota-2, -3, and -4 as super potent and broad-spectrum therapeutic nanobody candidates against COVID-19.

Ye, G., Pan, R., Bu, F., Zheng, J., Mendoza, A., Wen, W., Du, L., Spiller, B., Wadzinski, B.E., Liu, B., Perlman, S., Li, F.

(2023) J Virol 97: e0144823-e0144823

• PubMed: 37855638 
• DOI: https://doi.org/10.1128/jvi.01448-23
• Primary Citation Related Structures: 
  8G72, 8G73, 8G74, 8G75


• PubMed Abstract: 
  

  The COVID-19 pandemic exposed limitations of conventional antibodies as therapeutics, including high cost, limited potency, ineffectiveness against new viral variants, and primary reliance on injection-only delivery. Nanobodies are single-domain antibodies with therapeutic potentials. We discovered three anti-SARS-CoV-2 nanobodies, named Nanosota-2, -3, and -4, from an immunized alpaca. Nanosota-2 is super potent against prototypic SARS-CoV-2, Nanosota-3 is highly potent against the omicron variant, and Nanosota-4 is effective against both SARS-CoV-1 and SARS-CoV-2. In addition to their super potency and combined broad antiviral spectrum, these nanobodies are cost-effective, can be easily adapted to new viral variants through phage display, and can potentially be administered as inhalers. The Nanosota series are powerful therapeutic candidates to combat circulating SARS-CoV-2 and prepare for possible future coronavirus pandemics.

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Organizational Affiliation: 
• Department of Pharmacology, University of Minnesota Medical School , Minneapolis, Minnesota, USA.
Center for Coronavirus Research, University of Minnesota , Minneapolis, Minnesota, USA.
Department of Microbiology and Immunology, University of Iowa , Iowa City, Iowa, USA.
Hormel Institute, University of Minnesota , Austin, Minnesota, USA.
Institute for Biomedical Sciences, Georgia State University , Atlanta, Georgia, USA.
Department of Pharmacology, Vanderbilt University School of Medicine , Nashville, Tennessee, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 450.47 kDa 
• Atom Count: 27,543 
• Modeled Residue Count: 3,447 
• Deposited Residue Count: 3,974 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanosota-3	A [auth E], D [auth C]	136	Vicugna pacos	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B [auth A], C [auth B], E [auth D]	1,234	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: 12		Go to GlyGen: P0DTC2-1

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	F [auth J], G [auth F], H [auth G], I [auth H], J [auth I], K, L, M, N, O, P	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 B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth D], IA [auth D], JA [auth D], KA [auth D], LA [auth D], MA [auth D], NA [auth D], OA [auth D], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], 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: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Ye, G., Bu, F., Liu, B., Li, F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI089728
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI110700

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary