biostudies-literatureLin MHU.S. Department of Health & Human Services | NIH | National Institute of General Medical SciencesNIGMS NIH HHSCancer Prevention and Research Institute of TexasKempner Predoctoral Fellowship5742https://www.ebi.ac.uk/biostudies/studies/S-EPMC9525679biostudies-literatureUnknown13(1)Integrator is a multi-subunit protein complex associated with RNA polymerase II (Pol II), with critical roles in noncoding RNA 3'-end processing and transcription attenuation of a broad collection of mRNAs. IntS11 is the endonuclease for RNA cleavage, as a part of the IntS4-IntS9-IntS11 Integrator cleavage module (ICM). Here we report a cryo-EM structure of the Drosophila ICM, at 2.74 Å resolution, revealing stable association of an inositol hexakisphosphate (IP₆) molecule. The IP₆ binding site is located in a highly electropositive pocket at an interface among all three subunits of ICM, 55 Å away from the IntS11 active site and generally conserved in other ICMs. We also confirmed IP₆ association with the same site in human ICM. IP₆ binding is noNature communicationsInositol hexakisphosphate is required for Integrator function.PMC9525679R01 GM134539R35 GM118093R01GM134539R35GM118093T32 GM135134RP170593Lin MHElrod NDHuang KLTong LWelle KAWagner EJJensen MKfalseInositol hexakisphosphate is required for Integrator function.Integrator is a multi-subunit protein complex associated with RNA polymerase II (Pol II), with critical roles in noncoding RNA 3'-end processing and transcription attenuation of a broad collection of mRNAs. IntS11 is the endonuclease for RNA cleavage, as a part of the IntS4-IntS9-IntS11 Integrator cleavage module (ICM). Here we report a cryo-EM structure of the Drosophila ICM, at 2.74 Å resolution, revealing stable association of an inositol hexakisphosphate (IP₆) molecule. The IP₆ binding site is located in a highly electropositive pocket at an interface among all three subunits of ICM, 55 Å away from the IntS11 active site and generally conserved in other ICMs. We also confirmed IP₆ association with the same site in human ICM. IP₆ binding is no2022-01-01T00:00:00Z2022 Sep2026-06-01T02:10:27.84Z2025-02-19T01:28:32.52ZS-EPMC95256793618047310.1038/s41467-022-33506-3