6GYM

Structure of a yeast closed complex with distorted DNA (CCdist)

Summary for 6GYM

• Entry DOI: 10.2210/pdb6gym/pdb
• EMDB information: 0092
• Descriptor: General transcription and DNA repair factor IIH helicase subunit XPD,General transcription and DNA repair factor IIH helicase subunit XPD,DNA repair helicase RAD3,DNA repair helicase RAD3,General transcription and DNA repair factor IIH helicase subunit XPD, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, ... (34 entities in total)
• Functional Keywords: rna polymerase ii, transcription initiation, promoter opening, transcription
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 31
• Total formula weight: 1297092.70

Authors

Dienemann, C.,Schwalb, B.,Schilbach, S.,Cramer, P. (deposition date: 2018-06-30, release date: 2018-12-05, Last modification date: 2024-11-13)

Primary citation

Dienemann, C.,Schwalb, B.,Schilbach, S.,Cramer, P.
Promoter Distortion and Opening in the RNA Polymerase II Cleft.
Mol. Cell, 73:97-106.e4, 2019

PubMed Abstract: Transcription initiation requires opening of promoter DNA in the RNA polymerase II (Pol II) pre-initiation complex (PIC), but it remains unclear how this is achieved. Here we report the cryo-electron microscopic (cryo-EM) structure of a yeast PIC that contains underwound, distorted promoter DNA in the closed Pol II cleft. The DNA duplex axis is offset at the upstream edge of the initially melted DNA region (IMR) where DNA opening begins. Unstable IMRs are found in a subset of yeast promoters that we show can still initiate transcription after depletion of the transcription factor (TF) IIH (TFIIH) translocase Ssl2 (XPB in human) from the nucleus in vivo. PIC-induced DNA distortions may thus prime the IMR for melting and may explain how unstable IMRs that are predicted in promoters of Pol I and Pol III can open spontaneously. These results suggest that DNA distortion in the polymerase cleft is a general mechanism that contributes to promoter opening.

PubMed: 30472190
DOI: 10.1016/j.molcel.2018.10.014

Experimental method

ELECTRON MICROSCOPY (6.7 Å)