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Structure paper

TitleStructures of mammalian RNA polymerase II pre-initiation complexes.
Journal, issue, pagesNature, Vol. 594, Issue 7861, Page 124-128, Year 2021
Publish dateApr 26, 2021
AuthorsShintaro Aibara / Sandra Schilbach / Patrick Cramer /
PubMed AbstractThe initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) ...The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) assembles with general transcription factors into a pre-initiation complex (PIC) that opens promoter DNA. Previous work provided the molecular architecture of the yeast and human PIC and a topological model for DNA opening by the general transcription factor TFIIH. Here we report the high-resolution cryo-electron microscopy structure of PIC comprising human general factors and Sus scrofa domesticus Pol II, which is 99.9% identical to human Pol II. We determine the structures of PIC with closed and opened promoter DNA at 2.5-2.8 Å resolution, and resolve the structure of TFIIH at 2.9-4.0 Å resolution. We capture the TFIIH translocase XPB in the pre- and post-translocation states, and show that XPB induces and propagates a DNA twist to initiate the opening of DNA approximately 30 base pairs downstream of the TATA box. We also provide evidence that DNA opening occurs in two steps and leads to the detachment of TFIIH from the core PIC, which may stop DNA twisting and enable RNA chain initiation.
External linksNature / PubMed:33902107
MethodsEM (single particle)
Resolution2.4 - 9.1 Å
Structure data

EMDB-12610, PDB-7nvr:
Human Mediator with RNA Polymerase II Pre-initiation complex
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-12611, PDB-7nvs:
RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal position
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-12612, PDB-7nvt:
RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-12613, PDB-7nvu:
RNA polymerase II core pre-initiation complex with open promoter DNA
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-12614, PDB-7nvv:
XPB-containing part of TFIIH in a post-translocated state (with ADP-BeF3)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-12615, PDB-7nvw:
TFIIH in a pre-translocated state (without ADP-BeF3)
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-12616, PDB-7nvx:
TFIIH in a post-translocated state (with ADP-BeF3)
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-12617, PDB-7nvy:
RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position
Method: EM (single particle) / Resolution: 7.3 Å

EMDB-12618, PDB-7nvz:
RNA polymerase II pre-initiation complex with closed promoter DNA in distal position
Method: EM (single particle) / Resolution: 7.2 Å

EMDB-12619, PDB-7nw0:
RNA polymerase II pre-initiation complex with open promoter DNA
Method: EM (single particle) / Resolution: 6.6 Å

EMDB-12620:
Focused refinement of the core RNA polymerase II pre-initiation complex in a consensus CC state (without ADP-BeF3)
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-12621:
Focused refinement of the core RNA polymerase II pre-initiation complex in a consensus OC state (with ADP-BeF3)
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-12622:
Focused refinement of the upstream complex for the RNA polymerase II pre-initiation complex in a consensus CC state (without ADP-BeF3)
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-12623:
Focused refinement of the upstream complex for the RNA polymerase II pre-initiation complex in a consensus OC state (with ADP-BeF3)
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-12624:
Focused refinement of XPB containing part of TFIIH in pre-translocated state (without ADP-BeF3)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-12625:
Focused refinement of XPD containing part of TFIIH in pre-translocated state (without ADP-BeF3)
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-12626:
Focused refinement of XPD containing part of TFIIH in post-translocated state (with ADP-BeF3)
Method: EM (single particle) / Resolution: 4 Å

EMDB-12627:
Focused refinement of the RNA polymerase II core pre-initiation complex in a consensus IC-like state (with ADP-BeF3)
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-12628:
Focused refinement of the upstream complex for the RNA polymerase II pre-initiation complex in a consensus IC-like state (with ADP-BeF3)
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-12629:
Focused refinement of the core RNA polymerase II pre-initiation complex with intermediary promoter DNA (with ADP-BeF3)
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-12630:
RNA polymerase II pre-initiation complex with intermediary promoter DNA
Method: EM (single particle) / Resolution: 9.1 Å

Chemicals

ChemComp-SF4:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

ChemComp-ZN:
ZINC ION / Zinc

ChemComp-MG:
MAGNESIUM ION / Magnesium

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

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

Source
  • homo sapiens (human)
  • sus scrofa (pig)
  • human mastadenovirus c
  • trichoplusia ni (cabbage looper)
  • Pig (pig)
  • unidentified adenovirus
KeywordsTRANSCRIPTION / Mediator complex / RNA polymerase II / TFIIH / Pre-initiation complex / Initiation

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