Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structure of RNA polymerase II pre-initiation complex at 2.9 Å defines initial DNA opening.
Journal, issue, pages	Cell, Vol. 184, Issue 15, Page 4064-4072.e28, Year 2021
Publish date	Jul 22, 2021
Authors	Sandra Schilbach / Shintaro Aibara / Christian Dienemann / Frauke Grabbe / Patrick Cramer /
PubMed Abstract	Transcription initiation requires assembly of the RNA polymerase II (Pol II) pre-initiation complex (PIC) and opening of promoter DNA. Here, we present the long-sought high-resolution structure of ...Transcription initiation requires assembly of the RNA polymerase II (Pol II) pre-initiation complex (PIC) and opening of promoter DNA. Here, we present the long-sought high-resolution structure of the yeast PIC and define the mechanism of initial DNA opening. We trap the PIC in an intermediate state that contains half a turn of open DNA located 30-35 base pairs downstream of the TATA box. The initially opened DNA region is flanked and stabilized by the polymerase "clamp head loop" and the TFIIF "charged region" that both contribute to promoter-initiated transcription. TFIIE facilitates initiation by buttressing the clamp head loop and by regulating the TFIIH translocase. The initial DNA bubble is then extended in the upstream direction, leading to the open promoter complex and enabling start-site scanning and RNA synthesis. This unique mechanism of DNA opening may permit more intricate regulation than in the Pol I and Pol III systems.
External links	Cell / PubMed:34133942
Methods	EM (single particle)
Resolution	2.6 - 3.6 Å
Structure data	12719 7o4i EMDB-12719, PDB-7o4i: Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Method: EM (single particle) / Resolution: 3.2 Å 12720 7o4j EMDB-12720, PDB-7o4j: Yeast RNA polymerase II transcription pre-initiation complex (consensus) Method: EM (single particle) / Resolution: 2.9 Å 12721 7o4k EMDB-12721, PDB-7o4k: Yeast TFIIH in the contracted state within the pre-initiation complex Method: EM (single particle) / Resolution: 3.6 Å 12722 7o4l EMDB-12722, PDB-7o4l: Yeast TFIIH in the expanded state within the pre-initiation complex Method: EM (single particle) / Resolution: 3.4 Å EMDB-12723: Focused refinement of the upstream complex region of a RNA polymerase II transcription pre-initiation assembly Method: EM (single particle) / Resolution: 3.2 Å EMDB-12724: Focused refinement of RNA polymerase II (10-subunit) - TFIIB - TFIIF region of a transcription pre-initiation assembly Method: EM (single particle) / Resolution: 2.8 Å EMDB-12725: Focused refinement of RNA polymerase II (10-subunit) - TFIIB region of a transcription pre-initiation assembly Method: EM (single particle) / Resolution: 2.6 Å 12743 7o72 EMDB-12743, PDB-7o72: Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Method: EM (single particle) / Resolution: 3.4 Å 12744 7o73 EMDB-12744, PDB-7o73: Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Method: EM (single particle) / Resolution: 3.4 Å 12745 7o75 EMDB-12745, PDB-7o75: Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Method: EM (single particle) / Resolution: 3.2 Å
Chemicals	ChemComp-SF4: IRON/SULFUR CLUSTER / Iron–sulfur cluster ChemComp-ZN: Unknown entry ChemComp-BEF: BERYLLIUM TRIFLUORIDE ION ChemComp-MG: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate
Source	saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast) synthetic construct (others) Baker's yeast (brewer's yeast) saccharomyces cerevisiae s288c (yeast) saccharomyces cerevisiae yjm984 (yeast)
Keywords	TRANSCRIPTION / Pre-initiation complex