8FD5

Nucleocapsid monomer structure from SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb8FD5/pdb
• EM Map EMD-29002: EMDB EMDataResource

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


• Deposited: 2022-12-02 Released: 2023-01-11 
• Deposition Author(s): Casasanta, M., Jonaid, G.M., Kaylor, L., Luqiu, W., DiCecco, L., Solares, M., Berry, S., Kelly, D.F.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.57 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Insights of the SARS-CoV-2 Nucleocapsid Protein: Implications for the Inner-workings of Rapid Antigen Tests.

Casasanta, M.A., Jonaid, G.M., Kaylor, L., Luqiu, W.Y., DiCecco, L.A., Solares, M.J., Berry, S., Dearnaley, W.J., Kelly, D.F.

(2023) Microsc Microanal 29: 649-657

• PubMed: 37749713 
• DOI: https://doi.org/10.1093/micmic/ozac036
• Primary Citation of Related Structures:  
  8FD5, 8FG2


• PubMed Abstract: 
  

  The nucleocapsid (N) protein is an abundant component of SARS-CoV-2 and a key analyte for lateral-flow rapid antigen tests. Here, we present new structural insights for the SARS-CoV-2 N protein using cryo-electron microscopy (EM) and molecular modeling tools. Epitope mapping based on structural data supported host-immune interactions in the C-terminal portion of the protein, while other regions revealed protein-protein interaction sites. Complementary modeling results suggested that N protein structures from known variants of concern (VOC) are nearly 100% conserved at specific antibody-binding sites. Collectively, these results suggest that rapid tests that target the nucleocapsid C-terminal domain should have similar accuracy across all VOCs. In addition, our combined structural modeling workflow may guide the design of immune therapies to counter viral processes as we plan for future variants and pandemics.

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Organizational Affiliation: 

Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.69 kDa 
• Atom Count: 3,214 
• Modelled Residue Count: 419 
• Deposited Residue Count: 419 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A	419	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9  Go to UniProtKB:  P0DTC9

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.57 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	ISOLDE

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-11 
Deposition Author(s): Casasanta, M., Jonaid, G.M., Kaylor, L., Luqiu, W., DiCecco, L., Solares, M., Berry, S., Kelly, D.F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA193578
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA227261
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA219700

Revision History  

• Version 1.0: 2023-01-11
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references