An integrated structural model of the DNA damage- responsive H3K4me3 binding WDR76:SPIN1 complex with the nucleosome

• 成果类型: Article
• 署名作者: Liu, Xingyu; Zhang, Ying; Wen, Zhihui; Hao, Yan; Banks, Charles A. S.; Cesare, Joseph; Bhattacharya, Saikat; Arvindekar, Shreyas; Lange, Jeffrey J.; Xie, Yixuan; Garcia, Benjamin A.; Slaughter, Brian D.; Unruh, Jay R.; Viswanath, Shruthi; Florens, Laurence; Workman, Jerry L.; Washburn, Michael P.
• 署名单位: Stowers Institute for Medical Research; University of Kansas; University of Kansas Medical Center; Tata Institute of Fundamental Research (TIFR); National Centre for Biological Sciences (NCBS); Washington University (WUSTL); University of Texas System; University of Texas Southwestern Medical Center; University of Kansas; University of Kansas Medical Center
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-8834
• DOI: 10.1073/pnas.2318601121
• 发表日期: 2024-08-13
• 关键词: protein identification technology; tudor-like domains; web server; histone; spectroscopy; RECOGNITION; methylation; proteomics; spindlin1; pathways

摘要

Serial capture affinity purification (SCAP) is a powerful method to isolate a specific protein complex. When combined with cross- linking mass spectrometry and computational approaches, one can build an integrated structural model of the isolated complex. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone reader that recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to a previous SCAP analysis of the SPIN1:SPINDOC complex, histones and the H3K4me3 mark were enriched with the WDR76:SPIN1 complex. Next, interaction network analysis of copurifying proteins and microscopy analysis revealed a potential role of the WDR76:SPIN1 complex in the DNA damage response. Since we detected 149 pairs of cross- links between WDR76, SPIN1, and histones, we then built an integrated structural model of the complex where SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Finally, we used the powerful Bayesian Integrative Modeling approach as implemented in the Integrative Modeling Platform to build a model ofWDR76 and SPIN1 bound to the nucleosome.