The study investigates the structural basis for RNA polymerase II (Pol II) ubiquitylation and inactivation in transcription-coupled repair (TCR). Using cryogenic electron microscopy, biochemical assays, and cell biology approaches, the researchers found that ELOF1 serves as an adaptor to stably position UVSSA and CRL4CSA on arrested Pol II, leading to ligase neddylation and activation of Pol II ubiquitylation. ELOF1 restructures the interaction network within the Pol II-TCR complex, positioning the CRL4CSA ligase in relation to its substrate. The C-terminus of UVSSA is essential for Pol II ubiquitylation and TCR, contributing to the stabilization of the UVSSA-CSA interface and binding to downstream DNA. The Zn-finger in UVSSA mimics the binding of TFIIIS to Pol II, preventing reactivation of backtracked Pol II by TFIIIS. The findings provide a structural basis for how ELOF1 guides TCR from transcription toward DNA repair by restructuring the TCR complex to promote UVSSA integration, Pol II ubiquitylation, Pol II inactivation, and TFIIH recruitment.The study investigates the structural basis for RNA polymerase II (Pol II) ubiquitylation and inactivation in transcription-coupled repair (TCR). Using cryogenic electron microscopy, biochemical assays, and cell biology approaches, the researchers found that ELOF1 serves as an adaptor to stably position UVSSA and CRL4CSA on arrested Pol II, leading to ligase neddylation and activation of Pol II ubiquitylation. ELOF1 restructures the interaction network within the Pol II-TCR complex, positioning the CRL4CSA ligase in relation to its substrate. The C-terminus of UVSSA is essential for Pol II ubiquitylation and TCR, contributing to the stabilization of the UVSSA-CSA interface and binding to downstream DNA. The Zn-finger in UVSSA mimics the binding of TFIIIS to Pol II, preventing reactivation of backtracked Pol II by TFIIIS. The findings provide a structural basis for how ELOF1 guides TCR from transcription toward DNA repair by restructuring the TCR complex to promote UVSSA integration, Pol II ubiquitylation, Pol II inactivation, and TFIIH recruitment.