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Rhino is the least understood component of ATR-DDR. Structural modeling and binding free energy calculations revealed structural remodeling involving Rad17, Rad9\u2013Hus1\u2013Rad1 (9\u20131\u20131), and Rhino during ATR-DDR progression. Biochemical and computational analyses revealed the competitive binding of Rad17 and Rhino to the 9\u20131\u20131 complex, suggesting a structural transition from the Rad17\u20139\u20131\u20131 complex to the Rhino\u20139\u20131\u20131 complex. The presence of two conserved KYxxL+ motifs in Rhino suggests that it bridges the two 9\u20131\u20131 complexes. This enables the polymerization of multiple 9\u20131\u20131 complexes through Rhino and explains the long-standing discrepancy between the conventional model and experimental observations of Rad17 and Rad9 foci. Furthermore, structural analysis of the Rad9 C-terminal tail revealed its ability to compete with both Rhino and Rad17, leading to disassembly of the checkpoint complex and providing a mechanism for checkpoint inactivation. Quantum chemical calculations revealed comparable binding free energies for intermediate complexes. These observations suggest that the Rad17\u20139\u20131\u20131\u2013Rhino complex undergoes energetically equivalent structural transitions, providing a mechanistic basis for the sequential progression of ATR-DDR.<\/jats:p>","DOI":"10.1093\/nar\/gkag093","type":"journal-article","created":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T12:14:23Z","timestamp":1769516063000},"source":"Crossref","is-referenced-by-count":1,"title":["Energetically equivalent structural transitions in the Rad17\u2013Rad9\u2013Hus1\u2013Rad1\u2013Rhino complex underlie the sequential progression from activation through maintenance to inactivation of the ATR-dependent DNA damage response"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-3126-8970","authenticated-orcid":false,"given":"Yasunori","family":"Fukumoto","sequence":"first","affiliation":[{"name":"Laboratory of Toxicology and Environmental Health, Graduate School of Pharmaceutical Sciences, Chiba University , 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