6KQD

Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 3 nt

Summary for 6KQD

• Entry DOI: 10.2210/pdb6kqd/pdb
• Descriptor: DNA-directed RNA polymerase subunit alpha, ZINC ION, 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE, ... (12 entities in total)
• Functional Keywords: thermus thermophilus, rna polymerase, initiation transcription complex, 3nt rna, transcription
• Biological source: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579); More
• Total number of polymer chains: 18
• Total formula weight: 890496.63

Authors

Zhang, Y.,Li, L.,Ebright, R.H. (deposition date: 2019-08-17, release date: 2020-03-11, Last modification date: 2024-05-29)

Primary citation

Li, L.,Molodtsov, V.,Lin, W.,Ebright, R.H.,Zhang, Y.
RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA, 117:5801-5809, 2020

PubMed Abstract: All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the "σ-finger" of the bacterial transcription initiation factor σ. The structures reveal that-for both the primary σ-factor and extracytoplasmic (ECF) σ-factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA-the "σ-finger" is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from ∼5 nt to ∼10 nt.

PubMed: 32127479
DOI: 10.1073/pnas.1920747117

Experimental method

X-RAY DIFFRACTION (3.3 Å)