9EZB

SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P67S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.237 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.

Dhamotharan, K.Korn, S.M.Wacker, A.Becker, M.A.Gunther, S.Schwalbe, H.Schlundt, A.

(2024) Nat Commun 15: 10656-10656

  • DOI: https://doi.org/10.1038/s41467-024-55024-0
  • Primary Citation of Related Structures:  
    9EVY, 9EWH, 9EXB, 9EZB, 9F5J, 9F5L, 9F7A, 9F7C, 9F83, 9FBG

  • PubMed Abstract: 

    The SARS-CoV-2 nucleocapsid protein is indispensable for viral RNA genome processing. Although the N-terminal domain (NTD) is suggested to mediate specific RNA-interactions, high-resolution structures with viral RNA are still lacking. Available hybrid structures of the NTD with ssRNA and dsRNA provide valuable insights; however, the precise mechanism of complex formation remains elusive. Similarly, the molecular impact of nucleocapsid NTD mutations that have emerged since 2019 has not yet been fully explored. Using crystallography and solution NMR, we investigate how NTD mutations influence structural integrity and RNA-binding. We find that both features rely on a core network of residues conserved in Betacoronaviruses, crucial for protein stability and communication among flexible loop-regions that facilitate RNA-recognition. Our comprehensive structural analysis demonstrates that contacts within this network guide selective RNA-interactions. We propose that the core network renders the NTD evolutionarily robust in stability and plasticity for its versatile RNA processing roles.


  • Organizational Affiliation

    Institute for Molecular Biosciences, Goethe University, Frankfurt, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoprotein
A, B, C, D
136Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC9 
Go to UniProtKB:  P0DTC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.237 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.789α = 90
b = 92.466β = 90
c = 96.393γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
REFMACrefinement
PDB-REDOrefinement
Cootmodel building
BUCCANEERmodel building
Aimlessdata scaling
pointlessdata scaling
STARANISOdata scaling
autoPROCdata reduction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySCHL2062/2-1 and 2-2
German Research Foundation (DFG)Germany161793742
Other governmentGoethe-Corona-Funds
Other governmentJohanna Quandt Young Academy at Goethe (stipend number 2019/AS01)

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release
  • Version 1.1: 2024-12-11
    Changes: Derived calculations
  • Version 1.2: 2024-12-18
    Changes: Database references