Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 78.86 kDa 
• Atom Count: 6,378 
• Modelled Residue Count: 696 
• Deposited Residue Count: 698 
• Unique protein chains: 1

 5S6X

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z2889976755

• PDB DOI:  https://doi.org/10.2210/pdb5S6X/pdb
• Deposition Group: G_1002184 (changed state) ExploreG_1002184

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


• Deposited: 2020-11-13 Released: 2020-11-25 
• Deposition Author(s): Godoy, A.S., Douangamath, A., Nakamura, A.M., Dias, A., Krojer, T., Noske, G.D., Gawiljuk, V.O., Fernandes, R.S., Fairhead, M., Powell, A., Dunnet, L., Aimon, A., Fearon, D., Brandao-Neto, J., Skyner, R., von Delft, F., Oliva, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.222 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

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 

• PubMed: 37115000 
• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridylate-specific endoribonuclease	A, B	349	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.1 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], E [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
WUG (Subject of Investigation/LOI)	D [auth A], F [auth B]	1-(2,4-dimethyl-1H-imidazol-5-yl)methanamine C6 H11 N3 GEZOFSFHYQGWNK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.222 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.478	α = 90
b = 150.478	β = 90
c = 111.25	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Godoy, A.S., Douangamath, A., Nakamura, A.M., Dias, A., Krojer, T., Noske, G.D., Gawiljuk, V.O., Fernandes, R.S., Fairhead, M., Powell, A., Dunnet, L., Aimon, A., Fearon, D., Brandao-Neto, J., Skyner, R., von Delft, F., Oliva, G.

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2023-05-10
  Changes: Database references