8F1J

SigN RNA polymerase early-melted intermediate bound to mismatch DNA fragment dhsU36mm2 (-12A)

Summary for 8F1J

• Entry DOI: 10.2210/pdb8f1j/pdb
• EMDB information: 28783 28784 28785
• Descriptor: DNA (36-MER), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... (10 entities in total)
• Functional Keywords: promoter-bound, initiation, dna melting, transcription bubble nucleation, transcription, transcription-dna complex, transcription/dna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 10
• Total formula weight: 491106.06

Authors

Mueller, A.U.,Chen, J.,Darst, S.A. (deposition date: 2022-11-05, release date: 2023-04-05, Last modification date: 2024-06-19)

Primary citation

Mueller, A.U.,Chen, J.,Wu, M.,Chiu, C.,Nixon, B.T.,Campbell, E.A.,Darst, S.A.
A general mechanism for transcription bubble nucleation in bacteria.
Proc.Natl.Acad.Sci.USA, 120:e2220874120-e2220874120, 2023

PubMed Abstract: Bacterial transcription initiation requires σ factors for nucleation of the transcription bubble. The canonical housekeeping σ factor, σ, nucleates DNA melting via recognition of conserved bases of the promoter -10 motif, which are unstacked and captured in pockets of σ. By contrast, the mechanism of transcription bubble nucleation and formation during the unrelated σ-mediated transcription initiation is poorly understood. Herein, we combine structural and biochemical approaches to establish that σ, like σ, captures a flipped, unstacked base in a pocket formed between its N-terminal region I (RI) and extra-long helix features. Strikingly, RI inserts into the nascent bubble to stabilize the nucleated bubble prior to engagement of the obligate ATPase activator. Our data suggest a general paradigm of transcription initiation that requires σ factors to nucleate an early melted intermediate prior to productive RNA synthesis.

PubMed: 36972428
DOI: 10.1073/pnas.2220874120

Experimental method

ELECTRON MICROSCOPY (2.6 Å)