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Structure paper

TitleStructural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Journal, issue, pagesMol Cell, Vol. 82, Issue 3, Page 660-676.e9, Year 2022
Publish dateFeb 3, 2022
AuthorsChun Yang / Rina Fujiwara / Hee Jong Kim / Pratik Basnet / Yunye Zhu / Jose J Gorbea Colón / Stefan Steimle / Benjamin A Garcia / Craig D Kaplan / Kenji Murakami /
PubMed AbstractPrevious structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous ...Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation.
External linksMol Cell / PubMed:35051353 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 7.6 Å
Structure data

23789

7mei

EMDB-23789, PDB-7mei:
Composite structure of EC+EC
Method: EM (single particle) / Resolution: 3.54 Å

23887

7mk9

EMDB-23887, PDB-7mk9:
Complex structure of trailing EC of EC+EC (trailing EC-focused)
Method: EM (single particle) / Resolution: 3.54 Å

23888

7mka

EMDB-23888, PDB-7mka:
Structure of EC+EC (leading EC-focused)
Method: EM (single particle) / Resolution: 3.54 Å

23904

7ml0

EMDB-23904, PDB-7ml0:
RNA polymerase II pre-initiation complex (PIC1)
Method: EM (single particle) / Resolution: 3.0 Å

23905

7ml1

EMDB-23905, PDB-7ml1:
RNA polymerase II pre-initiation complex (PIC2)
Method: EM (single particle) / Resolution: 4.0 Å

23906

7ml2

EMDB-23906, PDB-7ml2:
RNA polymerase II pre-initiation complex (PIC3)
Method: EM (single particle) / Resolution: 3.4 Å

23907

7ml3

EMDB-23907, PDB-7ml3:
General transcription factor TFIIH (weak binding)
Method: EM (single particle) / Resolution: 7.6 Å

23908

7ml4

EMDB-23908, PDB-7ml4:
RNA polymerase II initially transcribing complex (ITC)
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-SF4:
IRON/SULFUR CLUSTER

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • baker's yeast (brewer's yeast)
KeywordsTRANSCRIPTION / pol II / PIC / TFIIH / ITC / RNA polymerase II

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