Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.55 kDa 
• Atom Count: 1,369 
• Modelled Residue Count: 154 
• Deposited Residue Count: 154 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 7ACS

The SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain in complex with 7mer dsRNA

• PDB DOI: 10.2210/pdb7ACS/pdb
• BMRB: 34511
• NDB: 7ACS

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


• Deposited: 2020-09-11 Released: 2020-11-04 
• Deposition Author(s): Veverka, V.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 30 
• Selection Criteria: structures with the least restraint violations 

Literature

Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein.

Dinesh, D.C., Chalupska, D., Silhan, J., Koutna, E., Nencka, R., Veverka, V., Boura, E.

(2020) PLoS Pathog 16: e1009100-e1009100

• PubMed: 33264373 
• DOI: 10.1371/journal.ppat.1009100
• Primary Citation of Related Structures:  
  6YI3, 7ACS, 7ACT


• PubMed Abstract: 
  

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19). SARS-CoV-2 is a single-stranded positive-sense RNA virus. Like other coronaviruses, SARS-CoV-2 has an unusually large genome that encodes four structural proteins and sixteen nonstructural proteins. The structural nucleocapsid phosphoprotein N is essential for linking the viral genome to the viral membrane. Both N-terminal RNA binding (N-NTD) and C-terminal dimerization domains are involved in capturing the RNA genome and, the intrinsically disordered region between these domains anchors the ribonucleoprotein complex to the viral membrane. Here, we characterized the structure of the N-NTD and its interaction with RNA using NMR spectroscopy. We observed a positively charged canyon on the surface of the N-NTD that might serve as a putative RNA binding site similarly to other coronaviruses. The subsequent NMR titrations using single-stranded and double-stranded RNA revealed a much more extensive U-shaped RNA-binding cleft lined with regularly distributed arginines and lysines. The NMR data supported by mutational analysis allowed us to construct hybrid atomic models of the N-NTD/RNA complex that provided detailed insight into RNA recognition.

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Organizational Affiliation: 

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A	140	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: N
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9  Go to UniProtKB:  P0DTC9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*AP*CP*UP*GP*AP*C)-3')	B	7	Severe acute respiratory syndrome coronavirus 2

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*UP*CP*AP*GP*UP*G)-3')	C	7	Severe acute respiratory syndrome coronavirus 2

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 30 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-04 
Deposition Author(s): Veverka, V.

Revision History  

• Version 1.0: 2020-11-04
  Type: Initial release
  
• Version 1.1: 2020-12-30
  Changes: Database references