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Structural basis of nucleosome remodeling by Cockayne syndrome B homologue Komagataella phaffii Rad26

Yutaro Fukushima, Chiaki Kinoshita, Lumi Negishi, Tomoya Kujirai, Yuki Kobayashi, Mitsuo Ogasawara, Haruhiko Ehara, Shun-ichi Sekine, Wataru Kagawa, Hitoshi Kurumizaka, Yoshimasa Takizawa

Abstract
Rad26, a yeast homologue of mammalian Cockayne syndrome protein B (CSB), plays an essential role in transcription-coupled nucleotide excision repair (TC-NER). Rad26/CSB binds RNA polymerase II stalled at DNA lesions and recruits DNA repair factors, functioning as a molecular scaffold. In addition, Rad26/CSB possesses nucleosome-remodeling activity that may help restore transcription after DNA repair. Here we determine the cryo-electron microscopy structure of the Rad26/CSB-nucleosome complex. Rad26/CSB binds near the nucleosomal entry/exit region (superhelical location +/-6) through a unique mechanism in which its ATPase domains, Lobe 1 and Lobe 2, engage nucleosomal DNA in a reverse orientation compared with other remodelers such as Snf2 and Ino80. Mutational, biochemical, and crosslinking mass-spectrometric analyses demonstrate the requirement of the KR loop for nucleosome binding and remodeling. Furthermore, we show that N-terminal auto-inhibition involves long-range contacts between the disordered N-terminus and the Lobe 2 region, and is relieved by mutations of Leu8 and Leu11. These findings reveal the structural basis of Rad26/CSB-mediated nucleosome remodeling in TC-NER.

Nature Communications, 17, 4881. doi: 10.1038/s41467-026-73500-7. (2026)
https://www.nature.com/articles/s41467-026-73500-7