Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 53.64 kDa 
• Atom Count: 3407 
• Modelled Residue Count: 438 
• Deposited Residue Count: 476 
• Unique protein chains: 2

6YVA

PLpro-C111S with mISG15

• PDB DOI: 10.2210/pdb6YVA/pdb

• Classification: CELL INVASION
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-04-28 Released: 2020-05-13 
• Deposition Author(s): Shin, D., Dikic, I.
• Funding Organization(s): German Research Foundation (DFG)

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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 

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

• PubMed: 32726803 
• 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 . 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.

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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 --: --

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Organizational Affiliation: 

Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, Frankfurt, Germany. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1a	A	315	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: rep, 1a-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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein ISG15	B [auth C]	161	Mus musculus	Mutation(s): 0  Gene Names: Isg15, G1p2, Ucrp
UniProt
Find proteins for Q64339 (Mus musculus) Explore Q64339  Go to UniProtKB:  Q64339

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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 = 157.047	α = 90
b = 157.047	β = 90
c = 83.633	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB1177

Revision History  

• 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