9HHH | pdb_00009hhh

A rare open conformation for Ubl2 domain of papain-like protease C111S of SARS-CoV2

PDB DOI: https://doi.org/10.2210/pdb9HHH/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-11-21 Released: 2025-12-10
Deposition Author(s): Freiherr von Scholley, G.L., Schaefer, M., Soler Lopez, M., Hillig, R., Mueller-Dieckmann, C., Kandiah, E.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.215 (Depositor), 0.215 (DCC)
R-Value Work:
0.179 (Depositor), 0.179 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural analysis of the flexibility of the Ubl2 domain within the papain-like protease of SARS-CoV-2.

Freiherr von Scholley, G.L., Schaefer, M., Tully, M.D., Hograindleur, M.A., Soler-Lopez, M., Hillig, R.C., Mueller-Dieckmann, C., Kandiah, E.

(2026) Acta Crystallogr F Struct Biol Commun 82: 222-230

PubMed: 42148530 Search on PubMed
DOI: https://doi.org/10.1107/S2053230X26003699
Primary Citation Related Structures:
9HHG, 9HHH, 9HHI

PubMed Abstract:
The papain-like protease (PLpro) of SARS-CoV-2 is part of the multi-domain nonstructural protein 3 (NSP3) and consists of two domains: a ubiquitin-like domain 2 (Ubl2) and a protease domain. PLpro plays a crucial role in the replication cycle of SARS-CoV-2, facilitating host immune-system evasion and the formation of double-membrane vesicles where replication occurs. While the function of the Ubl2 domain is still not clear, it is critical for the stability and the functional efficiency of PLpro. Despite its predicted inherent flexibility, nearly all SARS-CoV-1 and SARS-CoV-2 PLpro crystal structures deposited in the Protein Data Bank show the Ubl2 domain in a highly similar, closed conformation against the catalytic domain. Here, we present a crystal structure of PLpro exhibiting Ubl2 in two distinct conformations: the well characterized closed state, where Ubl2 is positioned near the PLpro domain, and an as yet uncharacterized open state, where Ubl2 is displaced by 4 Å from the PLpro core. This conformational variability in our structure appears to be related to the occupancy of a zinc ion within the zinc-finger domain. These results provide new insights into the flexibility of Ubl2, suggesting potential avenues for targeting and harnessing this dynamic behaviour for drug discovery.

Organizational Affiliation

European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, 38000 Grenoble, France.

Macromolecule Content

Total Structure Weight: 73.89 kDa
Atom Count: 5,599
Modeled Residue Count: 635
Deposited Residue Count: 644
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B	322	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1 Go to UniProtKB: P0DTC1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	F [auth A], G [auth A], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	C [auth A], D [auth A], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]