PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with FUZS-5

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

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Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.

Godoy, A.S.Nakamura, A.M.Douangamath, A.Song, Y.Noske, G.D.Gawriljuk, V.O.Fernandes, R.S.Pereira, H.D.M.Oliveira, K.I.Z.Fearon, D.Dias, A.Krojer, T.Fairhead, M.Powell, A.Dunnet, L.Brandao-Neto, J.Skyner, R.Chalk, R.Bajusz, D.Bege, M.Borbas, A.Keseru, G.M.von Delft, F.Oliva, G.

(2023) Nucleic Acids Res 

  • DOI: https://doi.org/10.1093/nar/gkad314
  • Primary Citation of Related Structures:  
    5S6X, 5S6Y, 5S6Z, 5S70, 5S71, 5S72, 5SA4, 5SA5, 5SA6, 5SA7, 5SA8, 5SA9, 5SAA, 5SAB, 5SAC, 5SAD, 5SAE, 5SAF, 5SAG, 5SAH, 5SAI, 5SBF, 7KEG, 7KEH, 7KF4, 7ME0, 7N7R, 7N7U, 7N7W, 7N7Y, 7N83, 7RB0, 7RB2

  • PubMed Abstract: 

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The NSP15 endoribonuclease enzyme, known as NendoU, is highly conserved and plays a critical role in the ability of the virus to evade the immune system. NendoU is a promising target for the development of new antiviral drugs. However, the complexity of the enzyme's structure and kinetics, along with the broad range of recognition sequences and lack of structural complexes, hampers the development of inhibitors. Here, we performed enzymatic characterization of NendoU in its monomeric and hexameric form, showing that hexamers are allosteric enzymes with a positive cooperative index, and with no influence of manganese on enzymatic activity. Through combining cryo-electron microscopy at different pHs, X-ray crystallography and biochemical and structural analysis, we showed that NendoU can shift between open and closed forms, which probably correspond to active and inactive states, respectively. We also explored the possibility of NendoU assembling into larger supramolecular structures and proposed a mechanism for allosteric regulation. In addition, we conducted a large fragment screening campaign against NendoU and identified several new allosteric sites that could be targeted for the development of new inhibitors. Overall, our findings provide insights into the complex structure and function of NendoU and offer new opportunities for the development of inhibitors.

  • Organizational Affiliation

    Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridylate-specific endoribonuclease
A, B
349Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.1
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.099α = 90
b = 150.099β = 90
c = 112.256γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Structure summary
  • Version 1.2: 2023-05-10
    Changes: Database references