5C4A

Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble

5C4A の概要

• エントリーDOI: 10.2210/pdb5c4a/pdb
• 関連するPDBエントリー: 5C3E 5C44 5C4J 5C4X
• 分子名称: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, ... (17 entities in total)
• 機能のキーワード: protein-dna complex, rna polymerase ii, transcribing complex, transcription bubble, transferase-rna-dna complex, transferase/rna/dna
• 由来する生物種: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); 詳細
• タンパク質・核酸の鎖数: 15
• 化学式量合計: 553168.16

構造登録者

Barnes, C.O.,Calero, M.,Malik, I.,Saphr, H.,Zhang, Q.,Pullara, F.,Kaplan, C.D.,Calero, G. (登録日: 2015-06-17, 公開日: 2015-08-26, 最終更新日: 2023-09-27)

主引用文献

Barnes, C.O.,Calero, M.,Malik, I.,Graham, B.W.,Spahr, H.,Lin, G.,Cohen, A.E.,Brown, I.S.,Zhang, Q.,Pullara, F.,Trakselis, M.A.,Kaplan, C.D.,Calero, G.
Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
Mol.Cell, 59:258-269, 2015

PubMed 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.

PubMed: 26186291
DOI: 10.1016/j.molcel.2015.06.034

実験手法

X-RAY DIFFRACTION (4.2 Å)