6XA9

SARS CoV-2 PLpro in complex with ISG15 C-terminal domain propargylamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2.

Klemm, T.Ebert, G.Calleja, D.J.Allison, C.C.Richardson, L.W.Bernardini, J.P.Lu, B.G.Kuchel, N.W.Grohmann, C.Shibata, Y.Gan, Z.Y.Cooney, J.P.Doerflinger, M.Au, A.E.Blackmore, T.R.van der Heden van Noort, G.J.Geurink, P.P.Ovaa, H.Newman, J.Riboldi-Tunnicliffe, A.Czabotar, P.E.Mitchell, J.P.Feltham, R.Lechtenberg, B.C.Lowes, K.N.Dewson, G.Pellegrini, M.Lessene, G.Komander, D.

(2020) EMBO J : e106275-e106275

  • DOI: 10.15252/embj.2020106275
  • Primary Citation of Related Structures:  
    6XA9, 6XAA

  • PubMed Abstract: 
  • The SARS-CoV-2 coronavirus encodes an essential papain-like protease domain as part of its non-structural protein (nsp)-3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin-like ISG15 protein modifications as well as, ...

    The SARS-CoV-2 coronavirus encodes an essential papain-like protease domain as part of its non-structural protein (nsp)-3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin-like ISG15 protein modifications as well as, with lower activity, Lys48-linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin-binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clinical compounds against SARS2 PLpro identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non-covalent small molecule SARS PLpro inhibitors also target SARS2 PLpro, prevent self-processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS-CoV-2 infection model.


    Related Citations: 
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution.
      Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C., Zwart, P.H.
      (2010) Acta Crystallogr D Biol Crystallogr 66: 213

    Organizational Affiliation

    The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Papain-like proteaseACE318Severe 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 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ISG15 CTD-propargylamideBDF80Homo sapiensMutation(s): 1 
Gene Names: ISG15G1P2UCRP
Find proteins for P05161 (Homo sapiens)
Explore P05161 
Go to UniProtKB:  P05161
NIH Common Fund Data Resources
PHAROS  P05161
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, C, E
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, C, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.172α = 90
b = 124.172β = 90
c = 238.169γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT1178122
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT2002119

Revision History 

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references, Derived calculations