8FTQ

Crystal structure of hRpn13 Pru domain in complex with Ubiquitin and XL44

Summary for 8FTQ

• Entry DOI: 10.2210/pdb8ftq/pdb
• Descriptor: Proteasomal ubiquitin receptor ADRM1, Ubiquitin, N-(3-{[(3R)-5-fluoro-2-oxo-2,3-dihydro-1H-indol-3-yl]methyl}phenyl)-4-methoxybenzamide, ... (4 entities in total)
• Functional Keywords: proteasome, rpn13, protac, protein binding
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 50387.26

Authors

Walters, K.J.,Lu, X.,Chandravanshi, M. (deposition date: 2023-01-13, release date: 2024-03-27, Last modification date: 2024-10-30)

Primary citation

Lu, X.,Chandravanshi, M.,Sabbasani, V.R.,Gaikwad, S.,Hughitt, V.K.,Gyabaah-Kessie, N.,Scroggins, B.T.,Das, S.,Myint, W.,Clapp, M.E.,Schwieters, C.D.,Dyba, M.A.,Bolhuis, D.L.,Koscielniak, J.W.,Andresson, T.,Emanuele, M.J.,Brown, N.G.,Matsuo, H.,Chari, R.,Citrin, D.E.,Mock, B.A.,Swenson, R.E.,Walters, K.J.
A structure-based designed small molecule depletes hRpn13 Pru and a select group of KEN box proteins.
Nat Commun, 15:2485-2485, 2024

PubMed Abstract: Proteasome subunit hRpn13 is partially proteolyzed in certain cancer cell types to generate hRpn13 by degradation of its UCHL5/Uch37-binding DEUBAD domain and retention of an intact proteasome- and ubiquitin-binding Pru domain. By using structure-guided virtual screening, we identify an hRpn13 binder (XL44) and solve its structure ligated to hRpn13 Pru by integrated X-ray crystallography and NMR to reveal its targeting mechanism. Surprisingly, hRpn13 is depleted in myeloma cells following treatment with XL44. TMT-MS experiments reveal a select group of off-targets, including PCNA clamp-associated factor PCLAF and ribonucleoside-diphosphate reductase subunit M2 (RRM2), that are similarly depleted by XL44 treatment. XL44 induces hRpn13-dependent apoptosis and also restricts cell viability by a PCLAF-dependent mechanism. A KEN box, but not ubiquitination, is required for XL44-induced depletion of PCLAF. Here, we show that XL44 induces ubiquitin-dependent loss of hRpn13 and ubiquitin-independent loss of select KEN box containing proteins.

PubMed: 38509117
DOI: 10.1038/s41467-024-46644-7

Experimental method

X-RAY DIFFRACTION (2.1 Å)