This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This lab has been working towards a solution of the cocrystal structure of RNA polymerase II-TFIIF complex. The transcription system of RNA polymerase II (Pol II) has emerged as an enormous protein apparatus consisting of the polymerase at its heart surrounded by layers of controlling factors. With recent crystallographic advances, it is now feasible to structurally characterize the apparatus in various complex forms, so we can understand Pol II-factor(s) interactions that modulate the activities of Pol II. Indeed, having a 'big picture' of how proteins interact in the Pol II machinery (a total of 50 polypeptides) and knowing the 'language' of their communication are the next challenges facing the structural biology of transcription. Using MacCHESS F1 and F2 stations, we have collected two native data sets to 7.5 from Pol II-TFIIF cocrystal with good statistics. Since the Pol II in the complex has been determined, we are now analyzing the data using protein phases generated from the polymerase model. Densities additional to Pol II model are clearly visible in three locations that could be arising from the TFIIF subunit, Tfg1, Tfg2 and Tfg3. More recently, we collected low-resolution data from cocrystals of another Pol II complex: the Pol II-capping enzyme complex. The capping enzyme catalyzes the formation of a special structure (the 5' cap) at the 5'-end of nascent RNA transcripts made by Pol II and is essential for cell vitality. Using combined phases from the Pol II model and an SAS set, we observed densities additional to the model structure and confined to a region adjacent to a helical domain of Pol II largest subunit Rpb1.
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