9NWT

Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A)

Summary for 9NWT

• Entry DOI: 10.2210/pdb9nwt/pdb
• EMDB information: 49893
• Descriptor: Sal-like protein 4, DNA damage-binding protein 1, Protein cereblon, ... (5 entities in total)
• Functional Keywords: ddb1, cereblon, mezigdomide, sall4, ligase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 163384.77

Authors

Park, J.,Hunkeler, M.,Roy Burman, S.S.,Fischer, E.S. (deposition date: 2025-03-24, release date: 2026-02-04)

Primary citation

Slabicki, M.,Park, J.,Nowak, R.P.,Roy Burman, S.S.,Pellman, J.,Zou, C.,Razumkov, H.,Carreiro, J.,Rastogi, S.,Goldstein, A.,Nagiec, M.M.,Donovan, K.A.,Che, J.,Hunkeler, M.,Geng, Q.,Hsu, C.L.,Lakshminarayan, M.,Shu, C.,Zon, R.L.,Kozicka, Z.,Park, P.M.C.,Tsai, J.M.,Yoon, H.,Jones, L.H.,Sperling, A.S.,Gray, N.S.,Fischer, E.S.,Ebert, B.L.
Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation.
Mol.Cell, 85:3184-3201.e14, 2025

PubMed Abstract: Glutarimide analogs, such as thalidomide, redirect the E3 ubiquitin ligase CRL4 to induce degradation of certain zinc finger (ZF) proteins. Although the core structural motif recognized by CRBN has been characterized, it does not fully explain substrate specificity. To explore the role of residues adjacent to this core motif, we constructed a comprehensive ZF reporter library of 9,097 reporters derived from 1,655 human ZF proteins and conducted a library-on-library screen with 29 glutarimide analogs to identify compounds that collectively degrade 38 ZF reporters. Cryo-electron microscopy and crystal structures of ZFs in complex with CRBN revealed the importance of interactions beyond the core ZF degron. We used systematic mutagenesis of ZFs and CRBN to identify modes of neosubstrate recruitment requiring distinct amino acids. Finally, we found subtle chemical variations in glutarimide analogs that alter target scope and selectivity, thus providing a roadmap for their rational design.

PubMed: 40845806
DOI: 10.1016/j.molcel.2025.07.019

Experimental method

ELECTRON MICROSCOPY (2.7 Å)