Crystal structure of the SARS CoV-1 Papain-like protease in complex with peptide inhibitor VIR250

Experimental Data Snapshot

  • Resolution: 2.29 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.229 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


A molecular sensor determines the ubiquitin substrate specificity of SARS-CoV-2 papain-like protease.

Patchett, S.Lv, Z.Rut, W.Bekes, M.Drag, M.Olsen, S.K.Huang, T.T.

(2021) Cell Rep 36: 109754-109754

  • DOI: https://doi.org/10.1016/j.celrep.2021.109754
  • Primary Citation of Related Structures:  
    7LFU, 7LFV

  • PubMed Abstract: 

    The SARS-CoV-2 papain-like protease (PLpro) is a target for antiviral drug development. It is essential for processing viral polyproteins for replication and functions in host immune evasion by cleaving ubiquitin (Ub) and ubiquitin-like protein (Ubl) conjugates. While highly conserved, SARS-CoV-2 and SARS-CoV PLpro have contrasting Ub/Ubl substrate preferences. Using a combination of structural analyses and functional assays, we identify a molecular sensor within the S1 Ub-binding site of PLpro that serves as a key determinant of substrate specificity. Variations within the S1 sensor specifically alter cleavage of Ub substrates but not of the Ubl interferon-stimulated gene 15 protein (ISG15). Significantly, a variant of concern associated with immune evasion carries a mutation in the S1 sensor that enhances PLpro activity on Ub substrates. Collectively, our data identify the S1 sensor region as a potential hotspot of variability that could alter host antiviral immune responses to newly emerging SARS-CoV-2 lineages.

  • Organizational Affiliation

    Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
papain-like proteaseA [auth D]325Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: 1a
EC: (PDB Primary Data), 3.4.22 (PDB Primary Data), (PDB Primary Data)
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X7
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Papain-like protease peptide inhibitor VIR250B [auth A]5synthetic constructMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on DPP
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 2.29 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.229 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.775α = 90
b = 90.408β = 90
c = 113.563γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM115568-06
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM128731-03
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR200030

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations