6PMI

Sigm28-transcription initiation complex with specific promoter at the state 1

Summary for 6PMI

• Entry DOI: 10.2210/pdb6pmi/pdb
• EMDB information: 20394
• Descriptor: DNA-directed RNA polymerase subunit alpha, MAGNESIUM ION, DNA-directed RNA polymerase subunit beta, ... (10 entities in total)
• Functional Keywords: sigma28, transcription initiation complex, rpof, znr domain, transcription
• Biological source: Escherichia coli O157:H7; More
• Total number of polymer chains: 9
• Total formula weight: 452738.92

Authors

Liu, B.,Shi, W. (deposition date: 2019-07-02, release date: 2020-05-13, Last modification date: 2024-03-20)

Primary citation

Shi, W.,Zhou, W.,Zhang, B.,Huang, S.,Jiang, Y.,Schammel, A.,Hu, Y.,Liu, B.
Structural basis of bacterial sigma28-mediated transcription reveals roles of the RNA polymerase zinc-binding domain.
Embo J., 39:e104389-e104389, 2020

PubMed Abstract: In bacteria, σ is the flagella-specific sigma factor that targets RNA polymerase (RNAP) to control the expression of flagella-related genes involving bacterial motility and chemotaxis. However, the structural mechanism of σ -dependent promoter recognition remains uncharacterized. Here, we report cryo-EM structures of E. coli σ -dependent transcribing complexes on a complete flagella-specific promoter. These structures reveal how σ -RNAP recognizes promoter DNA through strong interactions with the -10 element, but weak contacts with the -35 element, to initiate transcription. In addition, we observed a distinct architecture in which the β' zinc-binding domain (ZBD) of RNAP stretches out from its canonical position to interact with the upstream non-template strand. Further in vitro and in vivo assays demonstrate that this interaction has the overall effect of facilitating closed-to-open isomerization of the RNAP-promoter complex by compensating for the weak interaction between σ4 and -35 element. This suggests that ZBD relocation may be a general mechanism employed by σ family factors to enhance transcription from promoters with weak σ4/-35 element interactions.

PubMed: 32484956
DOI: 10.15252/embj.2020104389

Experimental method

ELECTRON MICROSCOPY (3.86 Å)