title: Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
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.
authors.affiliation: 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.
authors.forename: Christopher O
authors.initials: CO
authors.lastname: Barnes
authors.affiliation: Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
authors.forename: Monica
authors.initials: M
authors.lastname: Calero
authors.affiliation: Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.
authors.forename: Indranil
authors.initials: I
authors.lastname: Malik
authors.affiliation: Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
authors.forename: Brian W
authors.initials: BW
authors.lastname: Graham
authors.affiliation: Max Planck Institute for Biology of Ageing, Gleueler Strasse 50a, Cologne 50931, Germany.
authors.forename: Henrik
authors.initials: H
authors.lastname: Spahr
authors.affiliation: Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
authors.forename: Guowu
authors.initials: G
authors.lastname: Lin
authors.affiliation: Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA.
authors.forename: Aina E
authors.initials: AE
authors.lastname: Cohen
authors.affiliation: Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
authors.forename: Ian S
authors.initials: IS
authors.lastname: Brown
authors.affiliation: Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
authors.forename: Qiangmin
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; RiMED Foundation, Palermo, Sicilia 90133, Italy.
authors.forename: Filippo
authors.initials: F
authors.lastname: Pullara
authors.affiliation: Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Trakselis
authors.affiliation: Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.
authors.forename: Craig D
authors.initials: CD
authors.lastname: Kaplan
authors.affiliation: Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA. Electronic address: guc9@pitt.edu.
authors.forename: Guillermo
authors.initials: G
authors.lastname: Calero
mesh_terms: D001483:Base Sequence; D018360:Crystallography, X-Ray; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D054730:Protein Interaction Domains and Motifs; D020836:Protein Structure, Quaternary; D021122:Protein Subunits; D012319:RNA Polymerase II / Q000737:chemistry* / Q000378:metabolism; D012331:RNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000378:metabolism; D055672:Static Electricity; D014158:Transcription, Genetic
chemical_list: D004271:DNA, Fungal; D021122:Protein Subunits; D012331:RNA, Fungal; D029701:Saccharomyces cerevisiae Proteins; D012319:RNA Polymerase II; C580821:RPB2 protein, S cerevisiae; D012321:DNA-Directed RNA Polymerases; C517510:RPB5 protein, S cerevisiae