Notwithstanding numerous published structures of RNA Polymerase II (Pol II), structural details of Pol II engaging a complete nucleic acid scaffold have been lacking. Here, we report the structures of TFIIF-stabilized transcribing Pol II complexes, r ...
Notwithstanding numerous published structures of RNA Polymerase II (Pol II), structural details of Pol II engaging a complete nucleic acid scaffold have been lacking. Here, we report the structures of TFIIF-stabilized transcribing Pol II complexes, revealing the upstream duplex and full transcription bubble. The upstream duplex lies over a wedge-shaped loop from Rpb2 that engages its minor groove, providing part of the structural framework for DNA tracking during elongation. At the upstream transcription bubble fork, rudder and fork loop 1 residues spatially coordinate strand annealing and the nascent RNA transcript. At the downstream fork, a network of Pol II interactions with the non-template strand forms a rigid domain with the trigger loop (TL), allowing visualization of its open state. Overall, our observations suggest that "open/closed" conformational transitions of the TL may be linked to interactions with the non-template strand, possibly in a synchronized ratcheting manner conducive to polymerase translocation.
Organizational Affiliation:
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA. Electronic address: guc9@pitt.edu.,Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.,Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA.,Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.,Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.,Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; RiMED Foundation, Palermo, Sicilia 90133, Italy.,Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA.,Max Planck Institute for Biology of Ageing, Gleueler Strasse 50a, Cologne 50931, Germany.
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