9E2U
Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3)
This is a non-PDB format compatible entry.
Summary for 9E2U
| Entry DOI | 10.2210/pdb9e2u/pdb |
| Descriptor | DNA damage-binding protein 1, Protein cereblon, Zinc finger protein Helios, ... (5 entities in total) |
| Functional Keywords | crbn, ddb1, ikzf2, alv1, degradation, e3 ligase, ligase, molecular glue |
| Biological source | Homo sapiens (human) More |
| Total number of polymer chains | 24 |
| Total formula weight | 1363486.13 |
| Authors | |
| 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 Cited by 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: 40845806DOI: 10.1016/j.molcel.2025.07.019 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (4.11 Å) |
Structure validation
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