9CO8

JN.1 spike/Nanosota-9 complex

• PDB DOI: https://doi.org/10.2210/pdb9CO8/pdb
• EM Map EMD-45773: EMDB EMDataResource

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


• Deposited: 2024-07-16 Released: 2024-11-20 
• 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: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate

Ye, G., Bu, F., Liu, B., Li, F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 473.49 kDa 
• Atom Count: 29,026 
• Modelled Residue Count: 3,657 
• Deposited Residue Count: 4,209 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth B], B [auth C], C [auth A]	1,253	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: 6		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanosota-9	D [auth E], E [auth F], F [auth D]	150	Vicugna pacos	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	G [auth V], H [auth W], I [auth X], J [auth G], K [auth H], L [auth I], M [auth K], N [auth L], O [auth M], P [auth N], Q [auth O], R [auth Q], S [auth R], T [auth S], U [auth T], V [auth U]	2		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI171954

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release