9G8I

Sumo-Darpin-A10-complex

Summary for 9G8I

• Entry DOI: 10.2210/pdb9g8i/pdb
• Descriptor: DARPin, Ubiquitin-like protein SMT3 (3 entities in total)
• Functional Keywords: ankyrin repeat, sumo, signaling protein
• Biological source: synthetic construct; More
• Total number of polymer chains: 4
• Total formula weight: 50494.67

Authors

Cakilkaya, B.,Wolf, E.,Boergel, A. (deposition date: 2024-07-23, release date: 2025-03-05, Last modification date: 2025-03-12)

Primary citation

Troster, V.,Wong, R.P.,Borgel, A.,Cakilkaya, B.,Renz, C.,Mockel, M.M.,Eifler-Olivi, K.,Marinho, J.,Reinberg, T.,Furler, S.,Schaefer, J.V.,Pluckthun, A.,Wolf, E.,Ulrich, H.D.
Custom affinity probes reveal DNA-damage-induced, ssDNA-independent chromatin SUMOylation in budding yeast.
Cell Rep, 44:115353-115353, 2025

PubMed Abstract: The small ubiquitin-related modifier SUMO regulates cellular processes in eukaryotes either by modulating individual protein-protein interactions or with relaxed substrate selectivity by group modification. Here, we report the isolation and characterization of designed ankyrin repeat protein (DARPin)-based affinity probes directed against budding yeast SUMO (Smt3). We validate selected DARPins as compartment-specific inhibitors or neutral detection agents. Structural characterization reveals a recognition mode distinct from that of natural SUMO interactors. In vivo application pinpoints Smt3's essential function to the nucleus and demonstrates DARPin-mediated sensitization toward various stress conditions. A subset of selected clones is validated as SUMOylation reporters in cells. In this manner, we identify a DNA-damage-induced nuclear SUMOylation response that-in contrast to previously reported chromatin group SUMOylation-is independent of single-stranded DNA and the SUMO-E3 Siz2 but depends on Mms21 and likely reflects late intermediates of homologous recombination. Thus, Smt3-specific DARPins can provide insight into the dynamics of SUMOylation in defined subcellular structures.

PubMed: 40019834
DOI: 10.1016/j.celrep.2025.115353

Experimental method

X-RAY DIFFRACTION (2.51 Å)