6ZSL

Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.

Newman, J.A.Douangamath, A.Yadzani, S.Yosaatmadja, Y.Aimon, A.Brandao-Neto, J.Dunnett, L.Gorrie-Stone, T.Skyner, R.Fearon, D.Schapira, M.von Delft, F.Gileadi, O.

(2021) Nat Commun 12: 4848-4848

  • DOI: 10.1038/s41467-021-25166-6
  • Primary Citation of Related Structures:  
    6ZSL, 7NIO, 7NN0, 7NNG

  • PubMed Abstract: 
  • There is currently a lack of effective drugs to treat people infected with SARS-CoV-2, the cause of the global COVID-19 pandemic. The SARS-CoV-2 Non-structural protein 13 (NSP13) has been identified as a target for anti-virals due to its high sequence conservation and essential role in viral replication ...

    There is currently a lack of effective drugs to treat people infected with SARS-CoV-2, the cause of the global COVID-19 pandemic. The SARS-CoV-2 Non-structural protein 13 (NSP13) has been identified as a target for anti-virals due to its high sequence conservation and essential role in viral replication. Structural analysis reveals two "druggable" pockets on NSP13 that are among the most conserved sites in the entire SARS-CoV-2 proteome. Here we present crystal structures of SARS-CoV-2 NSP13 solved in the APO form and in the presence of both phosphate and a non-hydrolysable ATP analog. Comparisons of these structures reveal details of conformational changes that provide insights into the helicase mechanism and possible modes of inhibition. To identify starting points for drug development we have performed a crystallographic fragment screen against NSP13. The screen reveals 65 fragment hits across 52 datasets opening the way to structure guided development of novel antiviral agents.


    Organizational Affiliation

    Centre for Medicines Discovery, University of Oxford, Oxford, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SARS-CoV-2 helicase NSP13B [auth A], A [auth B]603Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.151α = 102.466
b = 70.12β = 95.646
c = 84.558γ = 112.79
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome Trust--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2021-10-20
    Changes: Data collection, Database references