9IOL

Cryo-EM structure of the complex of DNA, Ku70/80, and laXLF.

Summary for 9IOL

• Entry DOI: 10.2210/pdb9iol/pdb
• EMDB information: 60744
• Descriptor: X-ray repair cross-complementing protein 5, X-ray repair cross-complementing protein 6, DNA (5'-D(P*CP*GP*CP*TP*GP*CP*CP*GP*AP*TP*TP*CP*GP*TP*CP*GP*AP*CP*CP*T)-3'), ... (7 entities in total)
• Functional Keywords: dna repair, nhej, complex, lactylation, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 5
• Total formula weight: 169170.58

Authors

Liang, S. (deposition date: 2024-07-09, release date: 2025-07-09, Last modification date: 2025-07-30)

Primary citation

Jin, M.,Huang, B.,Yang, X.,Wang, S.,Wu, J.,He, Y.,Ding, X.,Wang, X.,Wang, Z.,Yang, J.,Li, R.,Zhou, X.,Wang, Q.,Li, Y.,Li, L.,Zheng, W.,Zeng, Z.,Zhao, C.,Liu, J.,Zhu, Q.,Kang, Z.,Li, K.,Liang, S.,Chen, Y.,Yuan, J.
Lactylation of XLF promotes non-homologous end-joining repair and chemoresistance in cancer.
Mol.Cell, 85:2654-2672.e7, 2025

PubMed Abstract: Metabolic reprogramming and DNA damage repair are essential in tumorigenesis and chemoresistance, yet their link remains elusive. Here, we show that LDHA deficiency impairs NHEJ and class switch recombination. Additionally, glycolysis-derived lactate promotes XLF lactylation at K288 within its Ku-binding motif (X-KBM) to regulate NHEJ. Mechanistically, DNA damage triggers ATM-mediated GCN5 phosphorylation to increase GCN5-XLF interaction and XLF lactylation, enhancing XLF-Ku80 binding, XLF recruitment to DSBs, and NHEJ efficiency. Cryo-EM structural analysis demonstrates that lactylated X-KBM (laX-KBM) forms a more extensive interface with Ku70/80, inducing conformational changes in the Ku80 vWA domain. XLF lactylation deficiency impairs NHEJ and sensitizes cancer cells to chemotherapy. A specific XLF K288 lactylation peptide inhibitor plus 5-fluorouracil synergistically kills colorectal cancer cells in PDX models with XLF hyperlactylation. These findings highlight that the GCN5-XLF lactylation axis is a critical NHEJ regulator and that targeting XLF lactylation can improve chemotherapy efficiency.

PubMed: 40680721
DOI: 10.1016/j.molcel.2025.06.019

Experimental method

ELECTRON MICROSCOPY (3.46 Å)