5L6B

Yeast 20S proteasome with mouse beta5i (1-138) and mouse beta6 (97-111; 118-133) in complex with ONX 0914

Summary for 5L6B

• Entry DOI: 10.2210/pdb5l6b/pdb
• Related: 5CZ4
• Related PRD ID: PRD_000991
• Descriptor: Proteasome subunit alpha type-2, Proteasome subunit beta type-4, Proteasome subunit beta type-8,Proteasome subunit beta type-5, ... (19 entities in total)
• Functional Keywords: hydrolase-hydrolase inhibitor complex, proteasome, mutant, inhibitor, binding analysis, hydrolase/hydrolase inhibitor
• Biological source: Mus musculus (Mouse); More
• Cellular location: Cytoplasm: P23639 P22141 P30656 P23724 P30657 P38624 P23638 P40303 P32379 P40302 P21242 P21243 P25043 P25451
• Total number of polymer chains: 28
• Total formula weight: 736021.92

Authors

Groll, M.,Huber, E.M. (deposition date: 2016-05-28, release date: 2016-11-09, Last modification date: 2024-01-10)

Primary citation

Huber, E.M.,Heinemeyer, W.,de Bruin, G.,Overkleeft, H.S.,Groll, M.
A humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit beta 5i.
EMBO J., 35:2602-2613, 2016

PubMed Abstract: Inhibition of the immunoproteasome subunit β5i alleviates autoimmune diseases in preclinical studies and represents a promising new anti-inflammatory therapy. However, the lack of structural data on the human immunoproteasome still hampers drug design. Here, we systematically determined the potency of seven α' β' epoxyketone inhibitors with varying N-caps and P3-stereochemistry for mouse/human β5c/β5i and found pronounced differences in their subunit and species selectivity. Using X-ray crystallography, the compounds were analyzed for their modes of binding to chimeric yeast proteasomes that incorporate key parts of human β5c, human β5i or mouse β5i and the neighboring β6 subunit. The structural data reveal exceptional conformations for the most selective human β5i inhibitors and highlight subtle structural differences as the major reason for the observed species selectivity. Altogether, the presented results validate the humanized yeast proteasome as a powerful tool for structure-based development of β5i inhibitors with potential clinical applications.

PubMed: 27789522
DOI: 10.15252/embj.201695222

Experimental method

X-RAY DIFFRACTION (2.6 Å)