7KHE

Escherichia coli RNA polymerase and rrnBP1 promoter pre-open complex with DksA/ppGpp

Replaces:  6WRG

Summary for 7KHE

• Entry DOI: 10.2210/pdb7khe/pdb
• EMDB information: 21883
• Descriptor: DNA-directed RNA polymerase subunit alpha, MAGNESIUM ION, ZINC ION, ... (12 entities in total)
• Functional Keywords: transcription, transcription-dna complex, transcription/dna
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 9
• Total formula weight: 498132.08

Authors

Shin, Y.,Qayyum, M.Z.,Murakami, K.S. (deposition date: 2020-10-21, release date: 2020-12-09, Last modification date: 2024-03-06)

Primary citation

Shin, Y.,Qayyum, M.Z.,Pupov, D.,Esyunina, D.,Kulbachinskiy, A.,Murakami, K.S.
Structural basis of ribosomal RNA transcription regulation.
Nat Commun, 12:528-528, 2021

PubMed Abstract: Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) σ holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized α subunit carboxyl-terminal domains and scrunches the template DNA with the σ finger and β' lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of σ domain 2 that opens a gate for DNA loading and ejects σ from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to σ ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp.

PubMed: 33483500
DOI: 10.1038/s41467-020-20776-y

Experimental method

ELECTRON MICROSCOPY (3.58 Å)