9N6N

Room Temperature X-Ray Structure of SARS-CoV-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Pomotrelvir

Summary for 9N6N

• Entry DOI: 10.2210/pdb9n6n/pdb
• Related: 9N6J 9N6L 9N6M
• Descriptor: 3C-like proteinase nsp5, Pomotrelvir bound form, SODIUM ION, ... (4 entities in total)
• Functional Keywords: cysteine protease, hydrolase
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 1
• Total formula weight: 34257.46

Authors

Bhandari, D.,Kovalevsky, A. (deposition date: 2025-02-05, release date: 2025-07-30)

Primary citation

Bhandari, D.,Gerlits, O.,Keable, S.,Coates, L.,Aniana, A.,Ghirlando, R.,Nashed, N.T.,Kovalevsky, A.,Louis, J.M.
Characterization of an unusual SARS-CoV-2 main protease natural variant exhibiting resistance to nirmatrelvir and ensitrelvir.
Commun Biol, 8:1061-1061, 2025

PubMed Abstract: We investigate the effects of two naturally selected substitution and deletion (Δ) mutations, constituting part of the substrate binding subsites S2 and S4, on the structure, function, and inhibition of SARS CoV-2 main protease. Comparable to wild-type, MPro undergoes N-terminal autoprocessing essential for stable dimer formation and mature-like catalytic activity. The structures are similar, but for an open active site conformation in MPro and increased dynamics of the S2 helix, S5 loop, and the helical domain. Some dimer interface contacts exhibit shorter H bond distances corroborating the ~40-fold enhanced dimerization of the mutant although its thermal sensitivity to unfolding is 8 °C lower, relative to wild-type. ITC reveals a 3- and 5-fold decrease in binding affinity for nirmatrelvir and ensitrelvir, respectively, and similar GC373 affinity, to MPro relative to wild-type. Structural differences in four inhibitor complexes of MPro compared to wild-type are described. Consistent with enhanced dynamics, the S2 helix and S5 loop adopting a more open conformation appears to be a unique feature of MPro both in the inhibitor-free and bound states. Our results suggest that mutational effects are compensated by changes in the conformational dynamics and thereby modulate N-terminal autoprocessing, K, catalytic efficiency, and inhibitor binding.

PubMed: 40676153
DOI: 10.1038/s42003-025-08487-w

Experimental method

X-RAY DIFFRACTION (1.85 Å)