6N58

Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation II

Summary for 6N58

• Entry DOI: 10.2210/pdb6n58/pdb
• EMDB information: 0348 0349
• Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... (9 entities in total)
• Functional Keywords: protein-dna complex, transcription initiation, rna polyermase, dna promoter melting, transcription, transferase
• Biological source: Escherichia coli; More
• Total number of polymer chains: 7
• Total formula weight: 473918.36

Authors

Chen, J.,Chiu, C.E.,Campbell, E.A.,Darst, S.A. (deposition date: 2018-11-21, release date: 2020-02-26, Last modification date: 2025-06-04)

Primary citation

Chen, J.,Gopalkrishnan, S.,Chiu, C.,Chen, A.Y.,Campbell, E.A.,Gourse, R.L.,Ross, W.,Darst, S.A.
E. coliTraR allosterically regulates transcription initiation by altering RNA polymerase conformation.
Elife, 8:-, 2019

PubMed Abstract: TraR and its homolog DksA are bacterial proteins that regulate transcription initiation by binding directly to RNA polymerase (RNAP) rather than to promoter DNA. Effects of TraR mimic the combined effects of DksA and its cofactor ppGpp, but the structural basis for regulation by these factors remains unclear. Here, we use cryo-electron microscopy to determine structures of RNAP, with or without TraR, and of an RNAP-promoter complex. TraR binding induced RNAP conformational changes not seen in previous crystallographic analyses, and a quantitative analysis revealed TraR-induced changes in RNAP conformational heterogeneity. These changes involve mobile regions of RNAP affecting promoter DNA interactions, including the βlobe, the clamp, the bridge helix, and several lineage-specific insertions. Using mutational approaches, we show that these structural changes, as well as effects on σ region 1.1, are critical for transcription activation or inhibition, depending on the kinetic features of regulated promoters.

PubMed: 31841111
DOI: 10.7554/eLife.49375

Experimental method

ELECTRON MICROSCOPY (3.78 Å)