6XAA

SARS CoV-2 PLpro in complex with ubiquitin propargylamide

• PDB DOI:  https://doi.org/10.2210/pdb6XAA/pdb

• Classification: HYDROLASE/SUBSTRATE
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-06-04 Released: 2020-06-17 
• Deposition Author(s): Klemm, T., Calleja, D.J., Richardson, L.W., Lechtenberg, B.C., Komander, D.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.260 
• R-Value Work: 0.210 
• R-Value Observed: 0.215 

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 39: e106275-e106275

• PubMed: 32845033 
• DOI: https://doi.org/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, 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 44.61 kDa 
• Atom Count: 3,023 
• Modelled Residue Count: 385 
• Deposited Residue Count: 394 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A	318	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22 (PDB Primary Data), 3.4.19.12 (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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-propargylamide	B	76	Homo sapiens	Mutation(s): 1  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.260 
• R-Value Work: 0.210 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.988	α = 90
b = 144.413	β = 90
c = 49.597	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data processing
Aimless	data scaling
Coot	model building
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Klemm, T., Calleja, D.J., Richardson, L.W., Lechtenberg, B.C., Komander, D.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT1178122
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT2002119

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2020-11-11
  Changes: Database references, Derived calculations
• Version 1.2: 2020-12-16
  Changes: Database references
• Version 1.3: 2021-01-27
  Changes: Structure summary