6JBQ

CryoEM structure of Escherichia coli sigmaE transcription initiation complex containing 5nt of RNA

Summary for 6JBQ

• Entry DOI: 10.2210/pdb6jbq/pdb
• EMDB information: 9792
• Descriptor: DNA-directed RNA polymerase subunit alpha, ZINC ION, DNA-directed RNA polymerase subunit beta, ... (10 entities in total)
• Functional Keywords: rna polymerase, extra-cytoplasmic function sigma factors, sigmae, transcription initiation, transcription-dna-rna complex, transcription/dna/rna
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 9
• Total formula weight: 447160.35

Authors

Fang, C.L.,Zhang, Y. (deposition date: 2019-01-26, release date: 2019-05-29, Last modification date: 2024-03-27)

Primary citation

Fang, C.,Li, L.,Shen, L.,Shi, J.,Wang, S.,Feng, Y.,Zhang, Y.
Structures and mechanism of transcription initiation by bacterial ECF factors.
Nucleic Acids Res., 47:7094-7104, 2019

PubMed Abstract: Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) σ factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 Å of Escherichia coli transcription initiation complex comprising σE-the most-studied bacterial ECF σ factor (Ec σE-RPo), and a crystal structure at 3.1 Å of Mycobacterium tuberculosis transcription initiation complex with a chimeric σH/E (Mtb σH/E-RPo). The structure of Ec σE-RPo reveals key interactions essential for assembly of E. coli σE-RNAP holoenzyme and for promoter recognition and unwinding by E. coli σE. Moreover, both structures show that the non-conserved linkers (σ2/σ4 linker) of the two ECF σ factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF σ factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such σ2/σ4 linker plays an important role in RPo formation, abortive production and promoter escape during ECF σ factors-mediated transcription initiation.

PubMed: 31131408
DOI: 10.1093/nar/gkz470

Experimental method

ELECTRON MICROSCOPY (4.02 Å)