Summary information and primary citation

PDB-id
7n4e; SNAP-derived features in text and JSON formats; DNAproDB
Class
transferase-DNA-RNA
Method
cryo-EM (3.8 Å)
Summary
Escherichia coli sigma 70-dependent paused transcription elongation complex
Reference
Pukhrambam C, Molodtsov V, Kooshkbaghi M, Tareen A, Vu H, Skalenko KS, Su M, Yin Z, Winkelman JT, Kinney JB, Ebright RH, Nickels BE (2022): "Structural and mechanistic basis of sigma-dependent transcriptional pausing." Proc.Natl.Acad.Sci.USA, 119, e2201301119. doi: 10.1073/pnas.2201301119.
Abstract
SignificanceThe paradigmatic example of factor-dependent pausing in transcription elongation is σ-dependent pausing, in which sequence-specific σ-DNA interaction with a - 10 element-like sequence in a transcribed region results in pausing of a σ-containing transcription elongation complex. It has been proposed that σ-dependent pausing involves DNA scrunching, and that sequences downstream of the -10 element-like sequence modulate DNA scrunching. Here, using site-specific protein-DNA photocrosslinking, high-throughput sequencing, and cryoelectron microscopy structure determination, we show directly that σ-dependent pausing involves DNA scrunching, we define a consensus sequence for formation of a stable scrunched paused complex that is identical to the consensus sequence for pausing in initial transcription, and we identify positions of DNA scrunching on DNA nontemplate and template strands. Our results illuminate the structural and mechanistic basis of σ-dependent transcriptional pausing.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js