7SD4

SARS-CoV-2 Nucleocapsid N-terminal domain (N-NTD) protein

• PDB DOI: https://doi.org/10.2210/pdb7SD4/pdb
• BMRB: 30955

• Classification: STRUCTURAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-09-29 Released: 2022-06-08 
• Deposition Author(s): Sarkar, S., Runge, B., Russell, R.W., Calero, D., Zeinalilathori, S., Quinn, C.M., Lu, M., Calero, G., Gronenborn, A.M., Polenova, T.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: SOLID-STATE NMR
• Conformers Calculated: 1000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Atomic-Resolution Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal Domain.

Sarkar, S., Runge, B., Russell, R.W., Movellan, K.T., Calero, D., Zeinalilathori, S., Quinn, C.M., Lu, M., Calero, G., Gronenborn, A.M., Polenova, T.

(2022) J Am Chem Soc 144: 10543-10555

• PubMed: 35638584 
• DOI: https://doi.org/10.1021/jacs.2c03320
• Primary Citation of Related Structures:  
  7SD4, 7UW3


• PubMed Abstract: 
  

  The nucleocapsid (N) protein is one of the four structural proteins of the SARS-CoV-2 virus and plays a crucial role in viral genome organization and, hence, replication and pathogenicity. The N-terminal domain (N ^NTD ) binds to the genomic RNA and thus comprises a potential target for inhibitor and vaccine development. We determined the atomic-resolution structure of crystalline N ^NTD by integrating solid-state magic angle spinning (MAS) NMR and X-ray diffraction. Our combined approach provides atomic details of protein packing interfaces as well as information about flexible regions as the N- and C-termini and the functionally important RNA binding, β-hairpin loop. In addition, ultrafast (100 kHz) MAS ¹ H-detected experiments permitted the assignment of side-chain proton chemical shifts not available by other means. The present structure offers guidance for designing therapeutic interventions against the SARS-CoV-2 infection.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content

• Total Structure Weight: 14.99 kDa 
• Atom Count: 1,061 
• Modelled Residue Count: 136 
• Deposited Residue Count: 136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A	136	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: SOLID-STATE NMR
• Conformers Calculated: 1000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Sarkar, S., Runge, B., Russell, R.W., Calero, D., Zeinalilathori, S., Quinn, C.M., Lu, M., Calero, G., Gronenborn, A.M., Polenova, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5P50AI150481
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5 P30 GM110758-02

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2022-06-15
  Changes: Database references
• Version 1.2: 2022-06-29
  Changes: Database references
• Version 1.3: 2023-06-14
  Changes: Advisory, Other