7LFV

Crystal structure of the SARS CoV-1 Papain-like protease in complex with peptide inhibitor VIR251

• PDB DOI: https://doi.org/10.2210/pdb7LFV/pdb

• Classification: Hydrolase/Hydrolas Inhibitor
• Organism(s): Severe acute respiratory syndrome-related coronavirus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-01-18 Released: 2021-11-10 
• Deposition Author(s): Olsen, S.K., Lv, Z.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cancer Prevention and Research Institute of Texas (CPRIT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.235 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

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

• PubMed: 34547223 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.11 kDa 
• Atom Count: 5,221 
• Modelled Residue Count: 636 
• Deposited Residue Count: 660 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
papain-like protease	A [auth B], B [auth A]	325	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: 1a EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data)
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7  Go to UniProtKB:  P0C6X7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease peptide inhibitor VIR251	C [auth D], D [auth F]	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	EA [auth A], R [auth B], S [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth B], U [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	AA [auth A], BA [auth A], CA [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], T [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	FA [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NH4	DA [auth A]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
73O	C [auth D], D [auth F]	L-PEPTIDE LINKING	C10 H13 N O3		TYR
DPP	C [auth D], D [auth F]	L-PEPTIDE LINKING	C3 H8 N2 O2		ALA

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002390	C [auth D], D [auth F]	Papain-like protease peptide inhibitor VIR251	Peptide-like / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.235 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.61	α = 90
b = 103.61	β = 90
c = 265.354	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-10 
Deposition Author(s): Olsen, S.K., Lv, Z.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM115568-06
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM128731-03
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR200030

Revision History  

• 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