6YVA

PLpro-C111S with mISG15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


This is version 2.3 of the entry. See complete history


Literature

Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity.

Shin, D.Mukherjee, R.Grewe, D.Bojkova, D.Baek, K.Bhattacharya, A.Schulz, L.Widera, M.Mehdipour, A.R.Tascher, G.Geurink, P.P.Wilhelm, A.van der Heden van Noort, G.J.Ovaa, H.Muller, S.Knobeloch, K.P.Rajalingam, K.Schulman, B.A.Cinatl, J.Hummer, G.Ciesek, S.Dikic, I.

(2020) Nature 587: 657-662

  • DOI: 10.1038/s41586-020-2601-5
  • Primary Citation of Related Structures:  
    6YVA

  • PubMed Abstract: 
  • The papain-like protease PLpro is an essential coronavirus enzyme that is required for processing viral polyproteins to generate a functional replicase complex and enable viral spread 1,2 . PLpro is also implicated in cleaving proteinaceous post-translational modifications on host proteins as an evasion mechanism against host antiviral immune responses 3-5 ...

    The papain-like protease PLpro is an essential coronavirus enzyme that is required for processing viral polyproteins to generate a functional replicase complex and enable viral spread 1,2 . PLpro is also implicated in cleaving proteinaceous post-translational modifications on host proteins as an evasion mechanism against host antiviral immune responses 3-5 . Here we perform biochemical, structural and functional characterization of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PLpro (SCoV2-PLpro) and outline differences with SARS-CoV PLpro (SCoV-PLpro) in regulation of host interferon and NF-κB pathways. SCoV2-PLpro and SCoV-PLpro share 83% sequence identity but exhibit different host substrate preferences; SCoV2-PLpro preferentially cleaves the ubiquitin-like interferon-stimulated gene 15 protein (ISG15), whereas SCoV-PLpro predominantly targets ubiquitin chains. The crystal structure of SCoV2-PLpro in complex with ISG15 reveals distinctive interactions with the amino-terminal ubiquitin-like domain of ISG15, highlighting the high affinity and specificity of these interactions. Furthermore, upon infection, SCoV2-PLpro contributes to the cleavage of ISG15 from interferon responsive factor 3 (IRF3) and attenuates type I interferon responses. Notably, inhibition of SCoV2-PLpro with GRL-0617 impairs the virus-induced cytopathogenic effect, maintains the antiviral interferon pathway and reduces viral replication in infected cells. These results highlight a potential dual therapeutic strategy in which targeting of SCoV2-PLpro can suppress SARS-CoV-2 infection and promote antiviral immunity.


    Related Citations: 
    • Inhibition of papain-like protease PLpro blocks SARS-CoV-2 spread and promotes anti-viral immunity
      Shin, D., Mukherjee, R., Grewe, D., Bojkova, D., Baek, K., Bhattacharya, A., Schulz, L., Widera, M., Mehdipour, A.R., Tascher, G., Geurink, P.P., van der Heden van Noort, G.J., Ovaa, H., Knobeloch, K.P., Rajalingam, K., Schulman, B.A., Cinatl, J., Hummer, G., Ciesek, S., Dikic, I.
      (2020) Nature --: --

    Organizational Affiliation

    Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, Frankfurt, Germany. dikic@biochem2.uni-frankfurt.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replicase polyprotein 1aA315Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
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 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like protein ISG15B [auth C]161Mus musculusMutation(s): 0 
Gene Names: Isg15G1p2Ucrp
UniProt
Find proteins for Q64339 (Mus musculus)
Explore Q64339 
Go to UniProtKB:  Q64339
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64339
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.047α = 90
b = 157.047β = 90
c = 83.633γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-04-28 
  • Released Date: 2020-05-13 
  • Deposition Author(s): Shin, D., Dikic, I.

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB1177

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 2.0: 2020-07-15
    Type: Coordinate replacement
    Reason: Real space R-factor
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2020-08-12
    Changes: Database references
  • Version 2.2: 2020-12-09
    Changes: Database references
  • Version 2.3: 2021-08-11
    Changes: Database references