7YWR

NMR structure of the N-terminal domain of Nsp8 from SARS-CoV-2


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

SARS-CoV-2 Nsp8 N-terminal domain folds autonomously and binds dsRNA.

Trevino, M.A.Pantoja-Uceda, D.Laurents, D.V.Mompean, M.

(2023) Nucleic Acids Res 51: 10041-10048

  • DOI: https://doi.org/10.1093/nar/gkad714
  • Primary Citation of Related Structures:  
    7YWR

  • PubMed Abstract: 

    The SARS-CoV-2 Nsp8 protein is a critical component of the RNA replicase, as its N-terminal domain (NTD) anchors Nsp12, the RNA, and Nsp13. Whereas its C-terminal domain (CTD) structure is well resolved, there is an open debate regarding the conformation adopted by the NTD as it is predicted as disordered but found in a variety of complex-dependent conformations or missing from many other structures. Using NMR spectroscopy, we show that the SARS CoV-2 Nsp8 NTD features both well folded secondary structure and disordered segments. Our results suggest that while part of this domain corresponding to two long α-helices forms autonomously, the folding of other segments would require interaction with other replicase components. When isolated, the α-helix population progressively declines towards the C-termini but surprisingly binds dsRNA while preserving structural disorder.


  • Organizational Affiliation

    "Blas Cabrera" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, Madrid 28006, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF1a polyprotein84Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: ORF1ab
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentSpainCOV20/00764

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Other
  • Version 1.2: 2024-06-19
    Changes: Data collection, Database references
  • Version 1.3: 2025-01-15
    Changes: Database references, Structure summary