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Structure paper

TitleStructure of RNA polymerase II pre-initiation complex at 2.9 Å defines initial DNA opening.
Journal, issue, pagesCell, Vol. 184, Issue 15, Page 4064-4072.e28, Year 2021
Publish dateJul 22, 2021
AuthorsSandra Schilbach / Shintaro Aibara / Christian Dienemann / Frauke Grabbe / Patrick Cramer /
PubMed AbstractTranscription 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 linksCell / PubMed:34133942
MethodsEM (single particle)
Resolution2.6 - 3.6 Å
Structure data

EMDB-12719, PDB-7o4i:
Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-12720, PDB-7o4j:
Yeast RNA polymerase II transcription pre-initiation complex (consensus)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-12721, PDB-7o4k:
Yeast TFIIH in the contracted state within the pre-initiation complex
Method: EM (single particle) / Resolution: 3.6 Å

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

EMDB-12743, PDB-7o72:
Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA
Method: EM (single particle) / Resolution: 3.4 Å

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

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

ChemComp-ZN:
Unknown entry

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • synthetic construct (others)
  • saccharomyces cerevisiae s288c (yeast)
  • saccharomyces cerevisiae yjm984 (yeast)
KeywordsTRANSCRIPTION / Pre-initiation complex

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