8PN9

Structure of human oligosaccharyltransferase OST-A complex bound to NGI-1

Summary for 8PN9

• Entry DOI: 10.2210/pdb8pn9/pdb
• EMDB information: 17779
• Descriptor: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (18 entities in total)
• Functional Keywords: n-glycosylation, ost-a complex, ngi-1 inhibitor, transferase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 8
• Total formula weight: 321362.22

Authors

Ramirez, A.S.,Kowal, J.,Locher, K.P. (deposition date: 2023-06-30, release date: 2024-05-08, Last modification date: 2024-11-13)

Primary citation

Lampson, B.L.,Ramirez, A.S.,Baro, M.,He, L.,Hegde, M.,Koduri, V.,Pfaff, J.L.,Hanna, R.E.,Kowal, J.,Shirole, N.H.,He, Y.,Doench, J.G.,Contessa, J.N.,Locher, K.P.,Kaelin Jr., W.G.
Positive selection CRISPR screens reveal a druggable pocket in an oligosaccharyltransferase required for inflammatory signaling to NF-kappa B.
Cell, 187:2209-2223.e16, 2024

PubMed Abstract: Nuclear factor κB (NF-κB) plays roles in various diseases. Many inflammatory signals, such as circulating lipopolysaccharides (LPSs), activate NF-κB via specific receptors. Using whole-genome CRISPR-Cas9 screens of LPS-treated cells that express an NF-κB-driven suicide gene, we discovered that the LPS receptor Toll-like receptor 4 (TLR4) is specifically dependent on the oligosaccharyltransferase complex OST-A for N-glycosylation and cell-surface localization. The tool compound NGI-1 inhibits OST complexes in vivo, but the underlying molecular mechanism remained unknown. We did a CRISPR base-editor screen for NGI-1-resistant variants of STT3A, the catalytic subunit of OST-A. These variants, in conjunction with cryoelectron microscopy studies, revealed that NGI-1 binds the catalytic site of STT3A, where it traps a molecule of the donor substrate dolichyl-PP-GlcNAc-Man-Glc, suggesting an uncompetitive inhibition mechanism. Our results provide a rationale for and an initial step toward the development of STT3A-specific inhibitors and illustrate the power of contemporaneous base-editor and structural studies to define drug mechanism of action.

PubMed: 38670073
DOI: 10.1016/j.cell.2024.03.022

Experimental method

ELECTRON MICROSCOPY (3.61 Å)