6UU3

E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP ("Old" crystal soaked with GTP, ATP, CTP, and ddTTP for 30 minutes)

This is a non-PDB format compatible entry.

Summary for 6UU3

• Entry DOI: 10.2210/pdb6uu3/pdb
• Descriptor: DNA-directed RNA polymerase subunit alpha, MAGNESIUM ION, CYTIDINE-5'-TRIPHOSPHATE, ... (12 entities in total)
• Functional Keywords: transcription initiation, rna polymerase, dna promoter, transcription bubble, de novo rna synthesis, dna scrunching, sigma-s factor, transcription, transferase-dna-rna complex, transferase/dna/rna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 9
• Total formula weight: 442149.13

Authors

Zuo, Y.,De, S.,Steitz, T.A. (deposition date: 2019-10-30, release date: 2020-08-26, Last modification date: 2023-10-11)

Primary citation

Zuo, Y.,De, S.,Feng, Y.,Steitz, T.A.
Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation.
Iscience, 23:101445-101445, 2020

PubMed Abstract: In bacteria, the dissociable σ subunit of the RNA polymerase (RNAP) is responsible for initiating RNA synthesis from specific DNA sites. As nascent RNA grows, downstream DNA unwinds and is pulled into the RNAP, causing stress accumulation and initiation complex destabilization. Processive transcription elongation requires at least partial separation of the σ factor from the RNAP core enzyme. Here, we present a series of transcription complexes captured between the early initiation and elongation phases via in-crystal RNA synthesis and cleavage. Crystal structures of these complexes indicate that stress accumulation during transcription initiation is not due to clashing of the growing nascent RNA with the σ loop, but results from scrunching of the template strand DNA that is contained inside the RNAP by the σ domain. Our results shed light on how scrunching of template-strand DNA drives both abortive initiation and σ-RNAP core separation to transition transcription from initiation to elongation.

PubMed: 32829286
DOI: 10.1016/j.isci.2020.101445

Experimental method

X-RAY DIFFRACTION (4.002 Å)