5C3E

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

Summary for 5C3E

• Entry DOI: 10.2210/pdb5c3e/pdb
• Descriptor: 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)
• Functional Keywords: protein-dna complex, rna polyermase ii, transcribing complex, transferase-dna-rna complex, transferase/dna/rna
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 15
• Total formula weight: 546388.20

Authors

Barnes, C.O.,Calero, M.,Malik, I.,Spahr, H.,Zhang, Q.,Pullara, F.,Kaplan, C.D.,Calero, G. (deposition date: 2015-06-17, release date: 2015-08-26, Last modification date: 2023-09-27)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (3.7 Å)