7N9C

Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes-CovS with NB95

• PDB DOI: https://doi.org/10.2210/pdb7N9C/pdb
• EM Map EMD-24256: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Lama glama
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-06-17 Released: 2021-08-04 
• Deposition Author(s): Sun, D., Zhang, C., Shi, Y.
• Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.71 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes

Sun, D., Sang, Z., Kim, Y.J., Xiang, Y., Cohen, T., Belford, A.K., Huet, A., Conway, J.F., Sun, J., Taylor, D.J., Schneidman-Duhovny, D., Zhang, C., Huang, W., Shi, Y.

(2021) Nat Commun 12: 4676

• DOI: https://doi.org/10.1038/s41467-021-24963-3

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 491.23 kDa 
• Atom Count: 22,734 
• Modelled Residue Count: 3,019 
• Deposited Residue Count: 4,450 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,380	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 9  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody NB95	D, E	155	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.71 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Sun, D., Zhang, C., Shi, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	R35 GM137905
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	R35 GM128641
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	U24 GM129539

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2021-08-11
  Changes: Database references