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TitleMechanism of nucleosomal H2A K13/15 monoubiquitination and adjacent dual monoubiquitination by RNF168.
Journal, issue, pagesNat Chem Biol, Vol. 21, Issue 5, Page 668-680, Year 2025
Publish dateOct 11, 2024
AuthorsHuasong Ai / Zebin Tong / Zhiheng Deng / Qiang Shi / Shixian Tao / Gaoge Sun / Jiawei Liang / Maoshen Sun / Xiangwei Wu / Qingyun Zheng / Lujun Liang / Hang Yin / Jia-Bin Li / Shuai Gao / Changlin Tian / Lei Liu / Man Pan /
PubMed AbstractThe DNA damage repair regulatory protein RNF168, a monomeric RING-type E3 ligase, has a crucial role in regulating cell fate and DNA repair by specific and efficient ubiquitination of the adjacent ...The DNA damage repair regulatory protein RNF168, a monomeric RING-type E3 ligase, has a crucial role in regulating cell fate and DNA repair by specific and efficient ubiquitination of the adjacent K13 and K15 (K13/15) sites at the H2A N-terminal tail. However, understanding how RNF168 coordinates with its cognate E2 enzyme UbcH5c to site-specifically ubiquitinate H2A K13/15 has long been hampered by the lack of high-resolution structures of RNF168 and UbcH5c~Ub (ubiquitin) in complex with nucleosomes. Here we developed chemical strategies and determined the cryo-electron microscopy structures of the RNF168-UbcH5c~Ub-nucleosome complex captured in transient H2A K13/15 monoubiquitination and adjacent dual monoubiquitination reactions, providing a 'helix-anchoring' mode for monomeric E3 ligase RNF168 on nucleosome in contrast to the 'compass-binding' mode of dimeric E3 ligases. Our work not only provides structural snapshots of H2A K13/15 site-specific monoubiquitination and adjacent dual monoubiquitination but also offers a near-atomic-resolution structural framework for understanding pathogenic amino acid substitutions and physiological modifications of RNF168.
External linksNat Chem Biol / PubMed:39394267
MethodsEM (single particle)
Resolution3.23 - 3.52 Å
Structure data

EMDB-39800: cryo-EM map of RNF168(1-193) in complex with Ubc5c-Ub conjugated nucleosome at a resolution of 3.23 angstrom
Method: EM (single particle) / Resolution: 3.23 Å

EMDB-60066: Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes (two Ub conformation)
Method: EM (single particle) / Resolution: 3.52 Å

Source
  • Homo sapiens (human)

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