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Mol Cell. 2015 Jul 16;59(2):258-69. doi: 10.1016/j.molcel.2015.06.034.

Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.

Author information

1
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.
2
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
3
Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.
4
Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
5
Max Planck Institute for Biology of Ageing, Gleueler Strasse 50a, Cologne 50931, Germany.
6
Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA.
7
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; RiMED Foundation, Palermo, Sicilia 90133, Italy.
8
Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA.
9
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA. Electronic address: guc9@pitt.edu.

Abstract

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.

PMID:
26186291
PMCID:
PMC4643057
DOI:
10.1016/j.molcel.2015.06.034
[Indexed for MEDLINE]
Free PMC Article

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