This study elucidates the structural basis for RNA polymerase II (Pol II) ubiquitylation and inactivation during transcription-coupled DNA repair (TCR). The research reveals that the elongation factor ELOF1 acts as an adaptor that stabilizes the positioning of the CRL4CSA ubiquitin ligase on arrested Pol II, facilitating its activation and enabling Pol II ubiquitylation. ELOF1 also positions a TFIIS-like element in UVSSA, which prevents reactivation of Pol II by TFIIS, thereby locking Pol II in an arrested state that allows DNA repair. The structural analysis shows that ELOF1 interacts with CSA and positions the CRL4CSA ligase in relation to its substrate, which is crucial for preventing off-target ubiquitylation events. The study further demonstrates that ELOF1 and UVSSA cooperatively drive Pol II ubiquitylation by stabilizing the docking and positioning of the CRL4CSA ligase on DNA damage-stalled Pol II. The neddylation of the CRL4CSA ligase is essential for its restructuring and efficient ubiquitylation of Pol II. The C-terminus of UVSSA is essential for its function, as it facilitates the integration of UVSSA into the Pol II-bound TCR complex. The UVSSA Zn-finger mimics TFIIS binding to Pol II, thereby inactivating arrested Pol II by blocking TFIIS access. The study provides a structural basis for the molecular mechanisms underlying TCR, highlighting the roles of ELOF1, UVSSA, and the CRL4CSA ligase in Pol II ubiquitylation and inactivation. The findings reveal how the TCR machinery suppresses Pol II reactivation to ensure DNA repair.This study elucidates the structural basis for RNA polymerase II (Pol II) ubiquitylation and inactivation during transcription-coupled DNA repair (TCR). The research reveals that the elongation factor ELOF1 acts as an adaptor that stabilizes the positioning of the CRL4CSA ubiquitin ligase on arrested Pol II, facilitating its activation and enabling Pol II ubiquitylation. ELOF1 also positions a TFIIS-like element in UVSSA, which prevents reactivation of Pol II by TFIIS, thereby locking Pol II in an arrested state that allows DNA repair. The structural analysis shows that ELOF1 interacts with CSA and positions the CRL4CSA ligase in relation to its substrate, which is crucial for preventing off-target ubiquitylation events. The study further demonstrates that ELOF1 and UVSSA cooperatively drive Pol II ubiquitylation by stabilizing the docking and positioning of the CRL4CSA ligase on DNA damage-stalled Pol II. The neddylation of the CRL4CSA ligase is essential for its restructuring and efficient ubiquitylation of Pol II. The C-terminus of UVSSA is essential for its function, as it facilitates the integration of UVSSA into the Pol II-bound TCR complex. The UVSSA Zn-finger mimics TFIIS binding to Pol II, thereby inactivating arrested Pol II by blocking TFIIS access. The study provides a structural basis for the molecular mechanisms underlying TCR, highlighting the roles of ELOF1, UVSSA, and the CRL4CSA ligase in Pol II ubiquitylation and inactivation. The findings reveal how the TCR machinery suppresses Pol II reactivation to ensure DNA repair.