9HHG

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

Summary for 9HHG

• Entry DOI: 10.2210/pdb9hhg/pdb
• Descriptor: Papain-like protease nsp3, GLYCEROL, ZINC ION, ... (5 entities in total)
• Functional Keywords: sars-cov2, plpro, enzyme, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 2
• Total formula weight: 73542.79

Authors

Freiherr von Scholley, G.L.,Schaefer, M.,Soler Lopez, M.,Hillig, R.,Mueller-Dieckmann, C.,Kandiah, E. (deposition date: 2024-11-21, release date: 2025-12-03, Last modification date: 2026-06-10)

Primary citation

Freiherr von Scholley, G.L.,Schaefer, M.,Tully, M.D.,Hograindleur, M.A.,Soler-Lopez, M.,Hillig, R.C.,Mueller-Dieckmann, C.,Kandiah, E.
Structural analysis of the flexibility of the Ubl2 domain within the papain-like protease of SARS-CoV-2.
Acta Crystallogr.,Sect.F, 82:222-230, 2026

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.

PubMed: 42148530
DOI: 10.1107/S2053230X26003699

Experimental method

X-RAY DIFFRACTION (1.95 Å)