9PFV

The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex

Summary for 9PFV

• Entry DOI: 10.2210/pdb9pfv/pdb
• EMDB information: 71615
• Descriptor: DNA-directed RNA polymerase subunit alpha, MAGNESIUM ION, ZINC ION, ... (11 entities in total)
• Functional Keywords: ccna_03891-ccna_01149 promoter transcription activation complex, drid, caulobacter, transcription, transcription-dna complex, transcription/dna
• Biological source: Caulobacter vibrioides NA1000; More
• Total number of polymer chains: 12
• Total formula weight: 604121.03

Authors

Singh, R.R.,Schumacher, M.A. (deposition date: 2025-07-06, release date: 2026-02-25, Last modification date: 2026-04-15)

Primary citation

Singh, R.R.,Chinni, A.,Cannistraci, E.,Salinas, R.,Yadav, S.,Gozzi, K.,Schumacher, M.A.
Transcription activation mechanism of a noncanonical DNA damage response pathway by the WYL-activator, DriD.
Sci Adv, 12:eaec6337-eaec6337, 2026

PubMed Abstract: DNA damage repair mechanisms are vital for cell survival. In the bacterium, , DriD is the master regulator of a unique, noncanonical DNA damage pathway. DriD binding to ssDNA, produced upon DNA damage, stimulates its ability to activate transcription from several promoters involved in DNA damage responses. However, the mechanism by which DriD interfaces with the RNAP holoenzyme to activate transcription from its multiple promoters has been unclear. Here, we describe cryo-EM structures of DriD-ssDNA bound to RNAP-holoenzyme and three DriD-regulated promoters. Each subunit of homodimeric DriD contains an DNA binding -terminal winged helix-turn-helix (wHTH) connected to WYL domains by a linker 3-helix bundle (3HB) module. The structures reveal a mechanism of assembly on promoters whereby DriD's 3HBs bind the RNAP α-CTD and β domains, anchoring the RNAP-holoenzyme to regulated promoters. The 3HBs form autoinhibitory contacts with DNABDs in apo DriD and therefore acts as an ssDNA-driven trigger domain, switching between DNABD-bound apo and RNAP-bound forms upon ssDNA-mediated activation. Thus, the structures reveal a unique transcription activation mechanism, likely conserved among the large family of homodimeric WYL activators.

PubMed: 41861017
DOI: 10.1126/sciadv.aec6337

Experimental method

ELECTRON MICROSCOPY (3.7 Å)